A Toolbox of Genetically Encoded FRET-Based Biosensors for Rapid l-Lysine Analysis

Optimizing Escherichia coli strains and fermentation processes for enhanced L-lysine production: a review

lysine is an essential amino acid with significant importance, widely used in the food, feed, and pharmaceutical industries. To meet the increasing demand, microbial fermentation has emerged as an effective and sustainable method for L-lysine production. Escherichia coli has become one of the primary microorganisms for industrial L-lysine production due to its rapid growth, ease of genetic manipulation, and high production efficiency. This paper reviews the recent advances in E. coli strain engineering and fermentation process optimization for L-lysine production. Additionally, it discusses potential technological breakthroughs and challenges in E. coli-based L-lysine production, offering directions for future research to support industrial-scale production.

Biosensors for the detection of chorismate and cis,cis-muconic acid in Corynebacterium glutamicum

Corynebacterium glutamicum ATCC 13032 is a promising microbial chassis for industrial production of valuable compounds, including aromatic amino acids derived from the shikimate pathway. In this work, we developed two whole-cell, transcription factor based fluorescent biosensors to track cis,cis-muconic acid (ccMA) and chorismate in C. glutamicum. Chorismate is a key intermediate in the shikimate pathway from which value-added chemicals can be produced, and a shunt from the shikimate pathway can divert carbon to ccMA, a high value chemical. We transferred a ccMA-inducible transcription factor, CatM, from Acinetobacter baylyi ADP1 into C. glutamicum and screened a promoter library to isolate variants with high sensitivity and dynamic range to ccMA by providing benzoate, which is converted to ccMA intracellularly. The biosensor also detected exogenously supplied ccMA, suggesting the presence of a putative ccMA transporter in C. glutamicum, though the external ccMA concentration threshold to elicit a response was 100-fold higher than the concentration of benzoate required to do so through intracellular ccMA production. We then developed a chorismate biosensor, in which a chorismate inducible promoter regulated by natively expressed QsuR was optimized to exhibit a dose-dependent response to exogenously supplemented quinate (a chorismate precursor). A chorismate-pyruvate lyase encoding gene, ubiC, was introduced into C. glutamicum to lower the intracellular chorismate pool, which resulted in loss of dose dependence to quinate. Further, a knockout strain that blocked the conversion of quinate to chorismate also resulted in absence of dose dependence to quinate, validating that the chorismate biosensor is specific to intracellular chorismate pool. The ccMA and chorismate biosensors were dually inserted into C. glutamicum to simultaneously detect intracellularly produced chorismate and ccMA. Biosensors, such as those developed in this study, can be applied in C. glutamicum for multiplex sensing to expedite pathway design and optimization through metabolic engineering in this promising chassis organism.

ONE-SENTENCE SUMMARY

High-throughput screening of promoter libraries in Corynebacterium glutamicum to establish transcription factor based biosensors for key metabolic intermediates in shikimate and β-ketoadipate pathways.

Retracing the evolution of a modern periplasmic binding protein

Investigating the evolution of structural features in modern multidomain proteins helps to understand their immense diversity and functional versatility. The class of periplasmic binding proteins (PBPs) offers an opportunity to interrogate one of the main processes driving diversification: the duplication and fusion of protein sequences to generate new architectures. The symmetry of their two-lobed topology, their mechanism of binding, and the organization of their operon structure led to the hypothesis that PBPs arose through a duplication and fusion event of a single common ancestor. To investigate this claim, we set out to reverse the evolutionary process and recreate the structural equivalent of a single-lobed progenitor using ribose-binding protein (RBP) as our model. We found that this modern PBP can be deconstructed into its lobes, producing two proteins that represent possible progenitor halves. The isolated halves of RBP are well folded and monomeric proteins, albeit with a lower thermostability, and do not retain the original binding function. However, the two entities readily form a heterodimer in vitro and in-cell. The x-ray structure of the heterodimer closely resembles the parental protein. Moreover, the binding function is fully regained upon formation of the heterodimer with a ligand affinity similar to that observed in the modern RBP. This highlights how a duplication event could have given rise to a stable and functional PBP-like fold and provides insights into how more complex functional structures can evolve from simpler molecular components.

Microfluidic single-cell scale-down systems: introduction, application, and future challenges

Performance losses during the scaling-up of bioprocesses from the laboratory to the production scale are common obstacles caused by the formation of concentration gradients in bioreactors. To overcome these obstacles, so-called scale-down bioreactors are used to analyze selected large-scale conditions and are one of the most important predictive tools for the successful transfer of bioprocesses from the lab to the industrial scale. In this regard, cellular behavior is usually measured as an averaged value, neglecting possible cell-to-cell heterogeneity within the culture. In contrast, microfluidic single-cell cultivation (MSCC) systems offer the possibility of understanding cellular processes on a single-cell level. To date, most MSCC systems have a limited choice of cultivation parameters that are not representative of bioprocess-relevant environmental conditions. Herein, we critically review recent advances in MSCC that allow the cultivation and analysis of cells under dynamic (bioprocess-relevant) environmental conditions. Finally, we discuss what technological advances and efforts are needed to bridge the gap between current MSCC systems and the use of these systems as single-cell scale-down devices.

Digital models in biotechnology: Towards multi-scale integration and implementation

Industrial biotechnology encompasses a large area of multi-scale and multi-disciplinary research activities. With the recent megatrend of digitalization sweeping across all industries, there is an increased focus in the biotechnology industry on developing, integrating and applying digital models to improve all aspects of industrial biotechnology. Given the rapid development of this field, we systematically classify the state-of-art modelling concepts applied at different scales in industrial biotechnology and critically discuss their current usage, advantages and limitations. Further, we critically analyzed current strategies to couple cell models with computational fluid dynamics to study the performance of industrial microorganisms in large-scale bioprocesses, which is of crucial importance for the bio-based production industries. One of the most challenging aspects in this context is gathering intracellular data under industrially relevant conditions. Towards comprehensive models, we discuss how different scale-down concepts combined with appropriate analytical tools can capture intracellular states of single cells. We finally illustrated how the efforts could be used to develop digitals models suitable for both cell factory design and process optimization at industrial scales in the future.

An L-2-hydroxyglutarate biosensor based on specific transcriptional regulator LhgR

l-2-Hydroxyglutarate (l-2-HG) plays important roles in diverse physiological processes, such as carbon starvation response, tumorigenesis, and hypoxic adaptation. Despite its importance and intensively studied metabolism, regulation of l-2-HG metabolism remains poorly understood and none of regulator specifically responded to l-2-HG has been identified. Based on bacterial genomic neighborhood analysis of the gene encoding l-2-HG oxidase (LhgO), LhgR, which represses the transcription of lhgO in Pseudomonas putida W619, is identified in this study. LhgR is demonstrated to recognize l-2-HG as its specific effector molecule, and this allosteric transcription factor is then used as a biorecognition element to construct an l-2-HG-sensing FRET sensor. The l-2-HG sensor is able to conveniently monitor the concentrations of l-2-HG in various biological samples. In addition to bacterial l-2-HG generation during carbon starvation, biological function of the l-2-HG dehydrogenase and hypoxia induced l-2-HG accumulation are also revealed by using the l-2-HG sensor in human cells.

L-2-hydroxyglutarate (L-2-HG) is an important metabolite but its regulation is poorly understood. Here the authors report an L-2-HG FRET biosensor based on the allosteric transcription factor, LhgR, to monitor L-2-HG in cells and biological samples.

Designing and Development of FRET-Based Nanosensor for Real Time Analysis of N-Acetyl-5-Neuraminic Acid in Living Cells

N-acetyl-5-neuraminic acid (NeuAc) plays crucial role in improving the growth, brain development, brain health maintenance, and immunity enhancement of infants. Commercially, it is used in the production of antiviral drugs, infant milk formulas, cosmetics, dietary supplements, and pharmaceutical products. Because of the rapidly increasing demand, metabolic engineering approach has attracted increasing attention for NeuAc biosynthesis. However, knowledge of metabolite flux in biosynthetic pathways is one of the major challenges in the practice of metabolic engineering. So, an understanding of the flux of NeuAc is needed to determine its cellular level at real time. The analysis of the flux can only be performed using a tool that has the capacity to measure metabolite level in cells without affecting other metabolic processes. A Fluorescence Resonance Energy Transfer (FRET)-based genetically-encoded nanosensor has been generated in this study to monitor the level of NeuAc in prokaryotic and eukaryotic cells. Sialic acid periplasmic binding protein (SiaP) from Haemophilus influenzae was exploited as a sensory element for the generation of nanosensor. The enhanced cyan fluorescent protein (ECFP) and Venus were used as Fluroscence Resonance Energy Transfer (FRET) pair. The nanosensor, which was termed fluorescent indicator protein for sialic acid (FLIP-SA), was successfully transformed into, and expressed in Escherichia coli BL21 (DE3) cells. The expressed protein of the nanosensor was isolated and purified. The purified nanosensor protein was characterized to assess the affinity, specificity, and stability in the pH range. The developed nanosensor exhibited FRET change after addition to NeuAc. The developed nanosensor was highly specific, exhibited pH stability, and detected NeuAc levels in the nanomolar to milimolar range. FLIP-SA was successfully introduced in bacterial and yeast cells and reported the real-time intracellular levels of NeuAc non-invasively. The FLIP-SA is an excellent tool for the metabolic flux analysis of the NeuAc biosynthetic pathway and, thus, may help unravel the regulatory mechanism of the metabolic pathway of NeuAc. Furthermore, FLIP-SA can be used for the high-throughput screening of E. coli mutant libraries for varied NeuAc production levels.

Linker Engineering in the Context of Synthetic Protein Switches and Sensors

Linkers play critical roles in the construction of synthetic protein switches and sensors as they functionally couple a receptor with an actuator. With an increasing number of molecular toolboxes and experimental strategies becoming available that can be applied to engineer protein switches and sensors with tailored response functions, optimising the connecting linkers remains an idiosyncratic and empiric process. This review aims to provide an in-depth analysis of linker motifs, the biophysical properties they confer, and how they impact the performance of synthetic protein switches and sensors while identifying trends, mechanisms, and strategies that underlie the most potent switches and sensors.

protaTETHER: A method for the incorporation of linkers in biomacromolecules

The impacts of linkers on dynamics, expression, and activity of biomacromolecules are often overlooked. This may be due, in part, to the lack of facile methods for incorporation and analysis of linkers that vary iteratively in both length and sequence composition. The protaTETHER method addresses this gap by enabling the incorporation of focused linker libraries at potentially any region in a protein sequence. In this chapter, we describe the generation and incorporation of linkers in a PKAc-GFP fusion protein and provide methods for the application and evaluation of the protaTETHER process.

The Role of Amino Acids in Neurotransmission and Fluorescent Tools for Their Detection

Neurotransmission between neurons, which can occur over the span of a few milliseconds, relies on the controlled release of small molecule neurotransmitters, many of which are amino acids. Fluorescence imaging provides the necessary speed to follow these events and has emerged as a powerful technique for investigating neurotransmission. In this review, we highlight some of the roles of the 20 canonical amino acids, GABA and β-alanine in neurotransmission. We also discuss available fluorescence-based probes for amino acids that have been shown to be compatible for live cell imaging, namely those based on synthetic dyes, nanostructures (quantum dots and nanotubes), and genetically encoded components. We aim to provide tool developers with information that may guide future engineering efforts and tool users with information regarding existing indicators to facilitate studies of amino acid dynamics.

Improvement of l-Valine Production by Atmospheric and Room Temperature Plasma Mutagenesis and High-Throughput Screening in Corynebacterium glutamicum

As one of the branched-chain amino acids, l-valine is an essential nutrient for most mammalian species. In this study, the l-valine producer Corynebacterium glutamicum ΔppcΔaceEΔalatΔpqo was first constructed. Additionally, an improved biosensor based on the Lrp-type transcriptional regulator and temperature-sensitive replication was built. Then, the C. glutamicum strain was mutagenized by atmospheric and room temperature plasma. A sequential three-step procedure was carried out to screen l-valine-producing strains, including the fluorescence-activated cell sorting (FACS), 96-well plate screening, and flask fermentation. The final mutant HL2-7 obtained by screening produced 3.20 g/L of l-valine, which was 21.47% higher than the titer produced by the starting strain. This study demonstrates that the l-valine-producing mutants can be successfully isolated based on the Lrp sensor system in combination with FACS screening after random mutagenesis.

A FRET-based biosensor for the quantification of glucose in culture supernatants of mL scale microbial cultivations

BACKGROUND

In most microbial cultivations D-glucose is the main carbon and energy source. However, quantification of D-glucose especially in small scale is still challenging. Therefore, we developed a FRET-based glucose biosensor, which can be applied in microbioreactor-based cultivations. This sensor consists of a glucose binding protein sandwiched between two fluorescent proteins, constituting a FRET pair. Upon D-glucose binding the sensor undergoes a conformational change which is translated into a FRET-ratio change.

RESULTS

The selected sensor shows an apparent Kd below 1.5 mM D-glucose and a very high sensitivity of up to 70% FRET-ratio change between the unbound and the glucose-saturated state. The soluble sensor was successfully applied online to monitor the glucose concentration in an Escherichia coli culture. Additionally, this sensor was utilized in an at-line process for a Corynebacterium glutamicum culture as an example for a process with cell-specific background (e.g. autofluorescence) and medium-induced quenching. Immobilization of the sensor via HaloTag® enabled purification and covalent immobilization in one step and increased the stability during application, significantly.

CONCLUSION

A FRET-based glucose sensor was used to quantify D-glucose consumption in microtiter plate based cultivations. To the best of our knowledge, this is the first method reported for online quantification of D-glucose in microtiter plate based cultivations. In comparison to D-glucose analysis via an enzymatic assay and HPLC, the sensor performed equally well, but enabled much faster measurements, which allowed to speed up microbial strain development significantly.

Impact of Molecular Crowding on Translational Mobility and Conformational Properties of Biological Macromolecules

Effects of molecular crowding on structural and dynamical properties of biological macromolecules do depend on the concentration of crowding agents but also on the molecular mass and the structural compactness of the crowder molecules. By employing fluorescence correlation spectroscopy (FCS), we investigated the translational mobility of several biological macromolecules ranging from 17 kDa to 2.7 MDa. Polyethylene glycol and Ficoll polymers of different molecular masses were used in buffer solutions to mimic a crowded environment. The reduction in translational mobility of the biological tracer molecules was analyzed as a function of crowder volume fractions and was generally more pronounced in PEG as compared to Ficoll solutions. For several crowding conditions, we observed a molecular sieving effect, in which the diffusion coefficient of larger tracer molecules is reduced to a larger extent than predicted by the Stokes-Einstein relation. By employing a FRET-based biosensor, we also showed that a multiprotein complex is significantly compacted in the presence of macromolecular crowders. Importantly, with respect to sensor in vivo applications, ligand concentration determining sensors would need a crowding specific calibration in order to deliver correct cytosolic ligand concentration.

Metabolic engineering advances and prospects for amino acid production

Amino acid fermentation is one of the major pillars of industrial biotechnology. The multi-billion USD amino acid market is rising steadily and is diversifying. Metabolic engineering is no longer focused solely on strain development for the bulk amino acids L-glutamate and L-lysine that are produced at the million-ton scale, but targets specialty amino acids. These demands are met by the development and application of new metabolic engineering tools including CRISPR and biosensor technologies as well as production processes by enabling a flexible feedstock concept, co-production and co-cultivation schemes. Metabolic engineering advances are exemplified for specialty proteinogenic amino acids, cyclic amino acids, omega-amino acids, and amino acids functionalized by hydroxylation, halogenation and N-methylation.

Single-Molecule Studies on a FRET Biosensor: Lessons from a Comparison of Fluorescent Protein Equipped versus Dye-Labeled Species

Bacterial periplasmic binding proteins (PBPs) undergo a pronounced ligand-induced conformational change which can be employed to monitor ligand concentrations. The most common strategy to take advantage of this conformational change for a biosensor design is to use a Förster resonance energy transfer (FRET) signal. This can be achieved by attaching either two fluorescent proteins (FPs) or two organic fluorescent dyes of different colors to the PBPs in order to obtain an optical readout signal which is closely related to the ligand concentration. In this study we compare a FP-equipped and a dye-labeled version of the glucose/galactose binding protein MglB at the single-molecule level. The comparison demonstrates that changes in the FRET signal upon glucose binding are more pronounced for the FP-equipped sensor construct as compared to the dye-labeled analog. Moreover, the FP-equipped sensor showed a strong increase of the FRET signal under crowding conditions whereas the dye-labeled sensor was not influenced by crowding. The choice of a labeling scheme should therefore be made depending on the application of a FRET-based sensor.

Genetically Encoded Förster Resonance Energy Transfer-Based Biosensors Studied on the Single-Molecule Level

Genetically encoded Förster resonance energy transfer (FRET)-based biosensors for the quantification of ligand molecules change the magnitude of FRET between two fluorescent proteins upon binding a target metabolite. When highly sensitive sensors are being designed, extensive sensor optimization is essential. However, it is often difficult to verify the ideas of modifications made to a sensor during the sensor optimization process because of the limited information content of ensemble FRET measurements. In contrast, single-molecule detection provides detailed information and higher accuracy. Here, we investigated a set of glucose and crowding sensors on the single-molecule level. We report the first comprehensive single-molecule study of FRET-based biosensors with reasonable counting statistics and identify characteristics in the single-molecule FRET histograms that constitute fingerprints of sensor performance. Hence, our single-molecule approach extends the toolbox of methods aiming to understand and optimize the design of FRET-based biosensors.

In vivo biosensors: mechanisms, development, and applications

In vivo biosensors can recognize and respond to specific cellular stimuli. In recent years, biosensors have been increasingly used in metabolic engineering and synthetic biology, because they can be implemented in synthetic circuits to control the expression of reporter genes in response to specific cellular stimuli, such as a certain metabolite or a change in pH. There are many types of natural sensing devices, which can be generally divided into two main categories: protein-based and nucleic acid-based. Both can be obtained either by directly mining from natural genetic components or by engineering the existing genetic components for novel specificity or improved characteristics. A wide range of new technologies have enabled rapid engineering and discovery of new biosensors, which are paving the way for a new era of biotechnological progress. Here, we review recent advances in the design, optimization, and applications of in vivo biosensors in the field of metabolic engineering and synthetic biology.

Population heterogeneity in microbial bioprocesses: origin, analysis, mechanisms, and future perspectives

Population heterogeneity is omnipresent in all bioprocesses even in homogenous environments. Its origin, however, is only so well understood that potential strategies like bet-hedging, noise in gene expression and division of labour that lead to population heterogeneity can be derived from experimental studies simulating the dynamics in industrial scale bioprocesses. This review aims at summarizing the current state of the different parts of single cell studies in bioprocesses. This includes setups to visualize different phenotypes of single cells, computational approaches connecting single cell physiology with environmental influence and special cultivation setups like scale-down reactors that have been proven to be useful to simulate large-scale conditions. A step in between investigation of populations and single cells is studying subpopulations with distinct properties that differ from the rest of the population with sub-omics methods which are also presented here. Moreover, the current knowledge about population heterogeneity in bioprocesses is summarized for relevant industrial production hosts and mixed cultures, as they provide the unique opportunity to distribute metabolic burden and optimize production processes in a way that is impossible in traditional monocultures. In the end, approaches to explain the underlying mechanism of population heterogeneity and the evidences found to support each hypothesis are presented. For instance, population heterogeneity serving as a bet-hedging strategy that is used as coordinated action against bioprocess-related stresses while at the same time spreading the risk between individual cells as it ensures the survival of least a part of the population in any environment the cells encounter.