Systematic optimization of L-tryptophan riboswitches for efficient monitoring of the metabolite in Escherichia coli

Algorithmic Programming of Sequential Logic and Genetic Circuits for Recording Biochemical Concentration in a Probiotic Bacterium

Through the implementation of designable genetic circuits, engineered probiotic microorganisms could be used as noninvasive diagnostic tools for the gastrointestinal tract. For these living cells to report detected biomarkers or signals after exiting the gut, the genetic circuits must be able to record these signals by using genetically encoded memory. Complex memory register circuits could enable multiplex interrogation of biomarkers and signals. A theory-based approach to create genetic circuits containing memory, known as sequential logic circuits, was previously established for a model laboratory strain of Escherichia coli, yet how circuit component performance varies for nonmodel and clinically relevant bacterial strains is poorly understood. Here, we develop a scalable computational approach to design robust sequential logic circuits in probiotic strain Escherichia coli Nissle 1917 (EcN). In this work, we used TetR-family transcriptional repressors to build genetic logic gates that can be composed into sequential logic circuits, along with a set of engineered sensors relevant for use in the gut environment. Using standard methods, 16 genetic NOT gates and nine sensors were experimentally characterized in EcN. These data were used to design and predict the performance of circuit designs. We present a set of genetic circuits encoding both combinational logic and sequential logic and show that the circuit outputs are in close agreement with our quantitative predictions from the design algorithm. Furthermore, we demonstrate an analog-like concentration recording circuit that detects and reports three input concentration ranges of a biochemical signal using sequential logic.

Molecular Complementarity of Proteomimetic Materials for Target-Specific Recognition and Recognition-Mediated Complex Functions

As biomolecules essential for sustaining life, proteins are generated from long chains of 20 different α-amino acids that are folded into unique 3D structures. In particular, many proteins have molecular recognition functions owing to their binding pockets, which have complementary shapes, charges, and polarities for specific targets, making these biopolymers unique and highly valuable for biomedical and biocatalytic applications. Based on the understanding of protein structures and microenvironments, molecular complementarity can be exhibited by synthesizable and modifiable materials. This has prompted researchers to explore the proteomimetic potentials of a diverse range of materials, including biologically available peptides and oligonucleotides, synthetic supramolecules, inorganic molecules, and related coordination networks. To fully resemble a protein, proteomimetic materials perform the molecular recognition to mediate complex molecular functions, such as allosteric regulation, signal transduction, enzymatic reactions, and stimuli-responsive motions; this can also expand the landscape of their potential bio-applications. This review focuses on the recognitive aspects of proteomimetic designs derived for individual materials and their conformations. Recent progress provides insights to help guide the development of advanced protein mimicry with material heterogeneity, design modularity, and tailored functionality. The perspectives and challenges of current proteomimetic designs and tools are also discussed in relation to future applications.

Genetically encoded biosensors for microbial synthetic biology: From conceptual frameworks to practical applications

Genetically encoded biosensors are the vital components of synthetic biology and metabolic engineering, as they are regarded as powerful devices for the dynamic control of genotype metabolism and evolution/screening of desirable phenotypes. This review summarized the recent advances in the construction and applications of different genetically encoded biosensors, including fluorescent protein-based biosensors, nucleic acid-based biosensors, allosteric transcription factor-based biosensors and two-component system-based biosensors. First, the construction frameworks of these biosensors were outlined. Then, the recent progress of biosensor applications in creating versatile microbial cell factories for the bioproduction of high-value chemicals was summarized. Finally, the challenges and prospects for constructing robust and sophisticated biosensors were discussed. This review provided theoretical guidance for constructing genetically encoded biosensors to create desirable microbial cell factories for sustainable bioproduction.

Modular tuning engineering and versatile applications of genetically encoded biosensors

Genetically encoded biosensors have a diverse range of detectable signals and potential applications in many fields, including metabolism control and high-throughput screening. Their ability to be used in situ with minimal interference to the bioprocess of interest could revolutionize synthetic biology and microbial cell factories. The performance and functions of these biosensors have been extensively studied and have been rapidly improved. We review here current biosensor tuning strategies and attempt to unravel how to obtain ideal biosensor functions through experimental adjustments. Strategies for expanding the biosensor input signals that increases the number of detectable compounds have also been summarized. Finally, different output signals and their practical requirements for biotechnology and biomedical applications and environmental safety concerns have been analyzed. This in-depth review of the responses and regulation mechanisms of genetically encoded biosensors will assist to improve their design and optimization in various application scenarios.

Unraveling the roles of plant specialized metabolites: using synthetic biology to design molecular biosensors

Plants are a rich source of specialized metabolites with a broad range of bioactivities and many applications in human daily life. Over the past decades significant progress has been made in identifying many such metabolites in different plant species and in elucidating their biosynthetic pathways. However, the biological roles of plant specialized metabolites remain elusive and proposed functions lack an identified underlying molecular mechanism. Understanding the roles of specialized metabolites frequently is hampered by their dynamic production and their specific spatiotemporal accumulation within plant tissues and organs throughout a plant's life cycle. In this review, we propose the employment of strategies from the field of Synthetic Biology to construct and optimize genetically encoded biosensors that can detect individual specialized metabolites in a standardized and high-throughput manner. This will help determine the precise localization of specialized metabolites at the tissue and single-cell levels. Such information will be useful in developing complete system-level models of specialized plant metabolism, which ultimately will demonstrate how the biosynthesis of specialized metabolites is integrated with the core processes of plant growth and development.

Signal amplification and optimization of riboswitch-based hybrid inputs by modular and titratable toehold switches

BACKGROUND

Synthetic biological circuits are widely utilized to control microbial cell functions. Natural and synthetic riboswitches are attractive sensor modules for use in synthetic biology applications. However, tuning the fold-change of riboswitch circuits is challenging because a deep understanding of the riboswitch mechanism and screening of mutant libraries is generally required. Therefore, novel molecular parts and strategies for straightforward tuning of the fold-change of riboswitch circuits are needed.

RESULTS

In this study, we devised a toehold switch-based modulator approach that combines a hybrid input construct consisting of a riboswitch and transcriptional repressor and de-novo-designed riboregulators named toehold switches. First, the introduction of a pair of toehold switches and triggers as a downstream signal-processing module to the hybrid input for coenzyme B12 resulted in a functional riboswitch circuit. Next, several optimization strategies that focused on balancing the expression levels of the RNA components greatly improved the fold-change from 260- to 887-fold depending on the promoter and host strain. Further characterizations confirmed low leakiness and high orthogonality of five toehold switch pairs, indicating the broad applicability of this strategy to riboswitch tuning.

CONCLUSIONS

The toehold switch-based modulator substantially improved the fold-change compared to the previous sensors with only the hybrid input construct. The programmable RNA-RNA interactions amenable to in silico design and optimization can facilitate further development of RNA-based genetic modulators for flexible tuning of riboswitch circuitry and synthetic biosensors.

Construction of a switchable synthetic Escherichia coli for aromatic amino acids by a tunable switch

Escherichia coli, a model microorganism for which convenient metabolic engineering tools are available and that grows quickly in cheap media, has been widely used in the production of valuable chemicals, including aromatic amino acids. As the three aromatic amino acids, L-tryptophan, L-tyrosine, and L-phenylalanine, share the same precursors, to increase the titer of a specific aromatic amino acid, the branch pathways to the others are usually permanently inactivated, which leads to the generation of auxotrophic strains. In this study, a tunable switch that can toggle between different states was constructed. Then, a switchable and non-auxotrophic E. coli strain for synthesis of aromatic amino acids was constructed using this tunable switch. By adding different inducers to cultures, three different production patterns of aromatic amino acids by the engineered strain could be observed. This tunable switch can also be applied in regulating other branch pathways and in other bacteria.

Contemporary Tools for Regulating Gene Expression in Bacteria

Insights from novel mechanistic paradigms in gene expression control have led to the development of new gene expression systems for bioproduction, control, and sensing applications. Coupled with a greater understanding of synthetic burden and modern creative biodesign approaches, contemporary bacterial gene expression tools and systems are emerging that permit fine-tuning of expression, enabling greater predictability and maximisation of specific productivity, while minimising deleterious effects upon cell viability. These advances have been achieved by using a plethora of regulatory tools, operating at all levels of the so-called 'central dogma' of molecular biology. In this review, we discuss these gene regulation tools in the context of their design, prototyping, integration into expression systems, and biotechnological application.

Molecular parts and genetic circuits for metabolic engineering of microorganisms

Microbial conversion of biomass into value-added biochemicals is a highly sustainable process compared to petroleum-based production. In this regard, microorganisms have been engineered via simple overexpression or deletion of metabolic genes to facilitate the production. However, the producer microorganisms require complex regulatory circuits to maximize productivity and performance. To address this issue, diverse genetic circuits have been developed that allow cells to minimize their metabolic burden, overcome metabolic imbalances and respond to a dynamically changing environment. In this review, we briefly explain the basic strategy for constructing genetic circuits by assembling molecular parts such as input, operation and output modules. Next, we describe recent applications of the circuits in the metabolic engineering of microorganisms to improve biochemical production. Beyond those achievements, genetic circuits will facilitate more innovative approaches to future strain development through mining and engineering new genetic elements and improving the complexity of genetic circuit design.

Riboswitch identification using Ligase-Assisted Selection for the Enrichment of Responsive Ribozymes (LigASERR)

In vitro selection of ligand-responsive ribozymes can identify rare, functional sequences from large libraries. While powerful, key caveats of this approach include lengthy and demanding experimental workflows; unpredictable experimental outcomes and unknown functionality of enriched sequences in vivo. To address the first of these limitations, we developed Ligase-Assisted Selection for the Enrichment of Responsive Ribozymes (LigASERR). LigASERR is scalable, amenable to automation and requires less time to implement compared to alternative methods. To improve the predictability of experiments, we modeled the underlying selection process, predicting experimental outcomes based on sequence and population parameters. We applied this new methodology and model to the enrichment of a known, in vitro-selected sequence from a bespoke library. Prior to implementing selection, conditions were optimized and target sequence dynamics accurately predicted for the majority of the experiment. In addition to enriching the target sequence, we identified two new, theophylline-activated ribozymes. Notably, all three sequences yielded riboswitches functional in Escherichia coli, suggesting LigASERR and similar in vitro selection methods can be utilized for generating functional riboswitches in this organism.

Recent advances and future trends of riboswitches: attractive regulatory tools

Bacterial genomes contain a huge amount of different genes. These genes are spatiotemporally expressed to accomplish some required functions within the organism. Inside the cell, any step of gene expression may be modulated at four possible places such as transcription initiation, translation regulation, mRNA stability and protein stability. To achieve this, there is a necessity of strong regulators either natural or synthetic which can fine-tune gene expression regarding the required function. In recent years, riboswitches as metabolite responsive control elements residing in the untranslated regions of certain messenger RNAs, have been known to control gene expression at transcription or translation level. Importantly, these control elements do not prescribe the involvement of protein factors for metabolite binding. However, they own their particular properties to sense intramolecular metabolites (ligands). Herein, we highlighted current important bacterial riboswitches, their applications to support genetic control, ligand-binding domain mechanisms and current progress in synthetic riboswitches.

Novel Hybrid Input Part Using Riboswitch and Transcriptional Repressor for Signal Inverting Amplifier

Genetic circuits are composed of input, logic, and output parts. Construction of complex circuits for practical applications requires numerous tunable genetic parts. However, the limited diversity and complicated tuning methods used for the input parts hinders the scalability of genetic circuits. Therefore, a new type of input part is required that responds to diverse signals and enables easy tuning. Here, we developed RNA-protein hybrid input parts that combine a riboswitch and orthogonal transcriptional repressors. The hybrid inputs successfully regulated the transcription of an output in response to the input signal detected by the riboswitch and resulted in signal inversion because of the expression of transcriptional repressors. Dose-response parameters including fold-change and half-maximal effective concentration were easily modulated and amplified simply by changing the promoter strength. Furthermore, the hybrid input detected both exogenous and endogenous signals, indicating potential applications in metabolite sensing. This hybrid input part could be highly extensible considering the rich variety of components.

Design rules of synthetic non-coding RNAs in bacteria

One of the long-term goals of synthetic biology is to develop designable genetic parts with predictable behaviors that can be utilized to implement diverse cellular functions. The discovery of non-coding RNAs and their importance in cellular processing have rapidly attracted researchers' attention towards designing functional non-coding RNA molecules. These synthetic non-coding RNAs have simple design principles governed by Watson-Crick base pairing, but exhibit increasingly complex functions. Importantly, due to their specific and modular behaviors, synthetic non-coding RNAs have been widely adopted to modulate transcription and translation of target genes. In this review, we summarize various design rules and strategies employed to engineer synthetic non-coding RNAs. Specifically, we discuss how RNA molecules can be transformed into powerful regulators and utilized to control target gene expression. With the establishment of generalizable non-coding RNA design rules, the research community will shift its focus to RNA regulators from protein regulators.

Genetic tool development and systemic regulation in biosynthetic technology

With the increased development in research, innovation, and policy interest in recent years, biosynthetic technology has developed rapidly, which combines engineering, electronics, computer science, mathematics, and other disciplines based on classical genetic engineering and metabolic engineering. It gives a wider perspective and a deeper level to perceive the nature of life via cell mechanism, regulatory networks, or biological evolution. Currently, synthetic biology has made great breakthrough in energy, chemical industry, and medicine industries, particularly in the programmable genetic control at multiple levels of regulation to perform designed goals. In this review, the most advanced and comprehensive developments achieved in biosynthetic technology were represented, including genetic engineering as well as synthetic genomics. In addition, the superiority together with the limitations of the current genome-editing tools were summarized.