Directed evolution of the PobR allosteric transcription factor to generate a biosensor for 4-hydroxymandelic acid

Biological Switches: Past and Future Milestones of Transcription Factor-Based Biosensors

Since the description of the lac operon in 1961 by Jacob and Monod, transcriptional regulation in prokaryotes has been studied extensively and has led to the development of transcription factor-based biosensors. Due to the broad variety of detectable small molecules and their various applications across biotechnology, biosensor research and development have increased exponentially over the past decades. Throughout this period, key milestones in fundamental knowledge, synthetic biology, analytical tools, and computational learning have led to an immense expansion of the biosensor repertoire and its application portfolio. Over the years, biosensor engineering became a more multidisciplinary discipline, combining high-throughput analytical tools, DNA randomization strategies, forward engineering, and advanced protein engineering workflows. Despite these advances, many obstacles remain to fully unlock the potential of biosensor technology. This review analyzes the timeline of key milestones on fundamental research (1960s to 2000s) and engineering strategies (2000s onward), on both the DNA and protein level of biosensors. Moreover, insights into the future perspectives, remaining hurdles, and unexplored opportunities of this promising field are discussed.

Directed evolution and metabolic engineering generate an Escherichia coli cell factory for de novo production of 4-hydroxymandelate

4-hydroxymandelate is a high-value aromatic compound used in the medicine, cosmetics, food, and chemical industry. However, existing natural extraction and chemical synthesis methods are costly and lead to environmental pollution. This study employed metabolic engineering and directed evolution strategies for de novo 4-hydroxymandelate biosynthesis. Two key challenges were addressed: insufficient precursor supply and limited activity of crucial enzymes. Through gene overexpression and multi-level gene interference using CRISPRi, An Escherichia coli chassis capable of producing the key precursor 4-hydroxyphenylpyruvate and the titer reached 5.05 mM (0.91 g/L). A mutant clone was obtained, HmaSV152G, which showed a 5.13-fold improvement in the catalytic rate. During fermentation, a high production of 194.87 mM (32.768 g/L) 4-hydroxymandelate was achieved in 76 h with a batch supply of glucose in a 5-L bioreactor. This study demonstrated the great potential of biosensors in protein engineering and provides a reference for large-scale production of other high-value aromatic compounds.

AI-Assisted Rational Design and Activity Prediction of Biological Elements for Optimizing Transcription-Factor-Based Biosensors

The rational design, activity prediction, and adaptive application of biological elements (bio-elements) are crucial research fields in synthetic biology. Currently, a major challenge in the field is efficiently designing desired bio-elements and accurately predicting their activity using vast datasets. The advancement of artificial intelligence (AI) technology has enabled machine learning and deep learning algorithms to excel in uncovering patterns in bio-element data and predicting their performance. This review explores the application of AI algorithms in the rational design of bio-elements, activity prediction, and the regulation of transcription-factor-based biosensor response performance using AI-designed elements. We discuss the advantages, adaptability, and biological challenges addressed by the AI algorithms in various applications, highlighting their powerful potential in analyzing biological data. Furthermore, we propose innovative solutions to the challenges faced by AI algorithms in the field and suggest future research directions. By consolidating current research and demonstrating the practical applications and future potential of AI in synthetic biology, this review provides valuable insights for advancing both academic research and practical applications in biotechnology.

Identifying LasR Quorum Sensors with Improved Signal Specificity by Mapping the Sequence-Function Landscape

Programmable intercellular signaling using components of naturally occurring quorum sensing can allow for coordinated functions to be engineered in microbial consortia. LuxR-type transcriptional regulators are widely used for this purpose and are activated by homoserine lactone (HSL) signals. However, they often suffer from imperfect molecular discrimination of structurally similar HSLs, causing misregulation within engineered consortia containing multiple HSL signals. Here, we studied one such example, the regulator LasR from Pseudomonas aeruginosa. We elucidated its sequence-function relationship for ligand specificity using targeted protein engineering and multiplexed high-throughput biosensor screening. A pooled combinatorial saturation mutagenesis library (9,486 LasR DNA sequences) was created by mutating six residues in LasR's β5 sheet with single, double, or triple amino acid substitutions. Sort-seq assays were performed in parallel using cognate and noncognate HSLs to quantify each corresponding sensor's response to each HSL signal, which identified hundreds of highly specific variants. Sensor variants identified were individually assayed and exhibited up to 60.6-fold (p = 0.0013) improved relative activation by the cognate signal compared to the wildtype. Interestingly, we uncovered prevalent mutational epistasis and previously unidentified residues contributing to signal specificity. The resulting sensors with negligible signal crosstalk could be broadly applied to engineer bacteria consortia.

Directed Evolution of 4-Hydroxyphenylpyruvate Biosensors Based on a Dual Selection System

Biosensors based on allosteric transcription factors have been widely used in synthetic biology. In this study, we utilized the Acinetobacter ADP1 transcription factor PobR to develop a biosensor activating the PpobA promoter when bound to its natural ligand, 4-hydroxybenzoic acid (4HB). To screen for PobR mutants responsive to 4-hydroxyphenylpyruvate(HPP), we developed a dual selection system in E. coli. The positive selection of this system was used to enrich PobR mutants that identified the required ligands. The following negative selection eliminated or weakened PobR mutants that still responded to 4HB. Directed evolution of the PobR library resulted in a variant where PobRW177R was 5.1 times more reactive to 4-hydroxyphenylpyruvate than PobRWT. Overall, we developed an efficient dual selection system for directed evolution of biosensors.

Modulating Sensitivity of an Erythromycin Biosensor for Precise High-Throughput Screening of Strains with Different Characteristics

Genetically encoded biosensors are powerful tools for product-driven high-throughput screening in synthetic biology and metabolic engineering. However, most biosensors can only properly function in a limited concentration cutoff, and the incompatible performance characteristics of biosensors will lead to false positives or failure in screening. The transcription factor (TF)-based biosensors are usually organized in modular architecture and function in a regulator-depended manner, whose performance properties can be fine-tuned by modifying the expression level of the TF. In this study, we modulated the performance characteristics, including sensitivity and operating range, of an MphR-based erythromycin biosensor by fine-adjusting regulator expression levels via ribosome-binding site (RBS) engineering and obtained a panel of biosensors with varied sensitivities by iterative fluorescence-assisted cell sorting (FACS) in Escherichia coli to accommodate different screening purposes. To exemplify their application potential, two engineered biosensors with 10-fold different sensitivities were employed in the precise high-throughput screening by microfluidic-based fluorescence-activated droplet sorting (FADS) of Saccharopolyspora erythraea mutant libraries with different starting erythromycin productions, and mutants representing as high as 6.8 folds and over 100% of production improvements were obtained starting from the wild-type strain and the high-producing industrial strain, respectively. This work demonstrated a simple strategy to engineer biosensor performance properties, which was significant to stepwise strain engineering and production improvement.