Transcription factor-based biosensors in biotechnology: current state and future prospects

Abstract

Living organisms have evolved a plethora of sensing systems for the intra- and extracellular detection of small molecules, ions or physical parameters. Several recent studies have demonstrated that these principles can be exploited to devise synthetic regulatory circuits for metabolic engineering strategies. In this context, transcription factors (TFs) controlling microbial physiology at the level of transcription play a major role in biosensor design, since they can be implemented in synthetic circuits controlling gene expression in dependency of, for example, small molecule production. Here, we review recent progress on the utilization of TF-based biosensors in microbial biotechnology highlighting different areas of application. Recent advances in metabolic engineering reveal TF-based sensors to be versatile tools for strain and enzyme development using high-throughput (HT) screening strategies and adaptive laboratory evolution, the optimization of heterologous pathways via the implementation of dynamic control circuits and for the monitoring of single-cell productivity in live cell imaging studies. These examples underline the immense potential of TF-based biosensor circuits but also identify limitations and room for further optimization.

Screening of an Escherichia coli promoter library for a phenylalanine biosensor

“…Thus, the higher the level of the transcriptional regulator, the more effector molecules can bind simultaneously resulting in a highly sensitive response and saturated operator sites at low concentrations. Likewise, the introduction of a second operator site or the modification of transcription factors were used to increase the sensitivity and dynamic range of sensor constructs in different studies (Lutz and Bujard 1997;Mahr and Frunzke 2016;Silva-Rocha and de Lorenzo 2012;Tabor et al 2009). The present study highlights the impact of the architecture of a biosensor on the sensor transfer curve and, thus, illustrates the necessity of comparative sensor design studies as prerequisite for an application in strain development or single-cell analysis.…”

“…During the last years, genetically encoded biosensors have revealed their potential as valuable tools for metabolic strain engineering and for enabling new insights into bioprocesses at single-cell resolution (Delvigne et al 2014;Liu et al 2015a;Mahr and Frunzke 2016;Schallmey et al 2014). By converting the intracellular effector molecule concentration into a measureable output, biosensors are in demand in cases, in which an easily detectable phenotype is not available.…”

“…Transcription factor (TF)-based biosensors consist of a regulator that is able to sense the level of an intra-or extracellular effector molecule and in turn drives the expression of a reporter gene (e.g., encoding an auto-fluorescent protein, AFP). By this means, accumulation of a certain effector can be converted into a measurable output signal (Mahr and Frunzke 2016). Biosensors based on bacterial TFs have successfully been implemented in high-throughput (HT) screenings of mutant libraries using fluorescence-activated cell sorting (FACS) (Binder et al 2012;Mustafi et al 2012;Siedler et al 2014) or in biosensor-driven adaptive evolution approaches for the improvement of microbial metabolite production (Mahr et al Electronic supplementary material The online version of this article (doi:10.1007/s00253-016-7575-8) contains supplementary material, which is available to authorized users.…”

“…In this context, biosensor-based strategies were shown to enable the identification of novel and non-intuitive targets for engineering and improving of production strains. Furthermore, the efficient screening of feedback-resistant enzymes (Schendzielorz et al 2014), dynamic pathway regulation (Dahl et al 2013;Liu et al 2015b;Xu et al 2014;Zhang et al 2012), and the analysis of population heterogeneity at the single-cell level (Hoffmann et al 2013;Mustafi et al 2014) demonstrate the broad applicability of biosensors (Liu et al 2015a;Mahr and Frunzke 2016).…”

Bacterial cell factoriest : applying thermophiles to fuel the biobased economy

“…Often results from simple 96-well plate assays are not sufficiently predictive to be useful. Several reporter systems have been developed that turn cells into fluorescent indicator strains for high productivity (Mahr & Frunzke, 2016;Yang et al, 2013). Still, the examples are all for titres that are well below industrially relevant ones, and it remains to be seen if the dynamic range of these biosensor systems can be stretched to be applied to select for improved strains at those high product concentrations.…”