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. ImportanceThe prevalence and persistence of PFAS in the environment is a growing area of concern. However, little is understood of the impacts of PFAS on the environment, particularly impacts on microorganisms that play pivotal roles in nearly every ecosystem. Thus, comprehensive measurements that provide systems-level insight into how microorganisms respond and adapt to PFAS in the environment are paramount. Here, we use RNA sequencing to study the global transcriptional response of E. coli MG1655 to two PFAS and non-fluorinated equivalent compounds across growth phases. We find that PFAS induce system-level changes in metabolic, transport, and gene regulatory pathways, providing insight into how these non-natural chemicals interact with a model bacterium. Additionally, the transcriptomic dataset associated with this work provides the community with PFSA-specific gene expression patterns and possible PFAS degradation pathways for the development of future whole-cell biosensors and mitigation efforts.