At-Home, Cell-Free Synthetic Biology Education Modules for Transcriptional Regulation and Environmental Water Quality Monitoring

Concentration-Dependent CsrA Regulation of the uxuB Transcript Leads to Development of a Post-Transcriptional Bandpass Filter

Post-transcriptional control systems offer new avenues for designing synthetic circuits that provide reduced burden and fewer synthetic regulatory components compared to transcriptionally based tools. Herein, we repurpose a newly identified post-transcriptional interaction between the uxuB mRNA transcript, specifically the 5' UTR + 100 nucleotides of coding sequence (100 nt CDS), and the E. coli Carbon Storage Regulatory A (CsrA) protein to design a biological post-transcriptional bandpass filter. In this work, we characterize the uxuB mRNA as a heterogeneous target of CsrA, where the protein can both activate and repress uxuB activity depending on its intracellular concentration. We leverage this interaction to implement a novel strategy of regulation within the 5' UTR of an mRNA. Specifically, we report a hierarchical binding strategy that may be leveraged by CsrA within uxuB to produce a dose-dependent response in regulatory outcomes. In our semisynthetic circuit, the uxuB 5' UTR + 100 nt CDS sequence is used as a scaffold that is fused to a gene of interest, which allows the circuit to transition between ON/OFF states based on the concentration range of free natively expressed CsrA. Notably, this system exerts regulation comparable to previously developed transcriptional bandpass filters while reducing the number of synthetic circuit components and can be used in concert with additional post-transcriptionally controlled circuits to achieve complex multi-signal control. We anticipate that future characterization of native regulatory RNA-protein systems will enable the development of more complex RNP-based circuits for synthetic biology applications.

Cell-Free Expression of Soluble Leafhopper Proteins from Brochosomes

Brochosomes are proteinaceous nanostructures produced by leafhopper insects with superhydrophobic and antireflective properties. Unfortunately, the production and study of brochosome-based materials has been limited by poor understanding of their major constituent subunit proteins, known as brochosomins, as well as their sensitivity to redox conditions due to essential disulfide bonds. Here, we used cell-free gene expression (CFE) to achieve recombinant production and analysis of brochosomin proteins. Through the optimization of redox environment, reaction temperature, and disulfide bond isomerase concentration, we achieved soluble brochosomin yields of up to 341 ± 30 μg/mL. Analysis using dynamic light scattering and transmission electron microscopy revealed distinct aggregation patterns among cell-free mixtures with different expressed brochosomins. We anticipate that the CFE methods developed here will accelerate the ability to change the geometries and properties of natural and modified brochosomes, as well as facilitate the expression and structural analysis of other poorly understood protein complexes.

Cell-Free Gene Expression: Methods and Applications

Cell-free gene expression (CFE) systems empower synthetic biologists to build biological molecules and processes outside of living intact cells. The foundational principle is that precise, complex biomolecular transformations can be conducted in purified enzyme or crude cell lysate systems. This concept circumvents mechanisms that have evolved to facilitate species survival, bypasses limitations on molecular transport across the cell wall, and provides a significant departure from traditional, cell-based processes that rely on microscopic cellular "reactors." In addition, cell-free systems are inherently distributable through freeze-drying, which allows simple distribution before rehydration at the point-of-use. Furthermore, as cell-free systems are nonliving, they provide built-in safeguards for biocontainment without the constraints attendant on genetically modified organisms. These features have led to a significant increase in the development and use of CFE systems over the past two decades. Here, we discuss recent advances in CFE systems and highlight how they are transforming efforts to build cells, control genetic networks, and manufacture biobased products.

Engineered transcription factor-binding diversed functional nucleic acid-based synthetic biosensor

Engineered transcription factors (eTFs) binding diversed functional nucleic acids (dFNAs), as innovative biorecognition systems, have gradually become indispensable core elements for building synthetic biosensors. They not only circumvent the limitations of the original TF-based biosensing technologies, but also inject new vitality into the field of synthetic biosensing. This review aims to provide the first comprehensive and systematic dissection of the eTF-dFNA synthetic biosensor concept. Firstly, the core principles and interaction mechanisms of eTF-dFNA biosensors are clarified. Next, we elaborate on the construction strategies of eTF-dFNA synthetic biosensors, detailing methods for the personalized customization of eTFs (irrational design, rational design, and semi-rational design) and dFNAs (SELEX, modifying and predicting), along with the exploration of strategies for the flexible selection of signal amplification and output modes. Furthermore, we discuss the exceptional performance and substantial advantages of eTF-dFNA synthetic biosensors, analyzing them from four perspectives: recognition domain, detection speed, sensitivity, and construction methodology. Building upon this analysis, we present their outstanding applications in point-of-care diagnostics, food-safety detection, environmental monitoring, and production control. Finally, we address the current limitations of eTF-dFNA synthetic biosensors candidly and envision the future direction of this technology, aiming to provide valuable insights for further research and applications in this burgeoning field.

Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory

The Cold Spring Harbor Laboratory (CSHL) Summer Course on Synthetic Biology, established in 2013, has emerged as a premier platform for immersive education and research in this dynamic field. Rooted in CSHL's rich legacy of biological discovery, the course offers a comprehensive exploration of synthetic biology's fundamentals and applications. Led by a consortium of faculty from diverse institutions, the course structure seamlessly integrates practical laboratory sessions, exploratory research rotations, and enriching seminars by leaders in the field. Over the years, the curriculum has evolved to cover essential topics such as cell-free transcription-translation, DNA construction, computational modeling of gene circuits, engineered gene regulation, and CRISPR technologies. In this review, we describe the history, development, and structure of the course, and discuss how elements of the course might inform the development of other short courses in synthetic biology. We also demonstrate the course's impact beyond the lab with a summary of alumni contributions to research, education, and entrepreneurship. Through these efforts, the CSHL Summer Course on Synthetic Biology remains at the forefront of shaping the next generation of synthetic biologists.

Cell-Free Translation Quantification via a Fluorescent Minihelix

Cell-free gene expression systems are used in numerous applications, including medicine making, diagnostics, and educational kits. Accurate quantification of nonfluorescent proteins in these systems remains a challenge. To address this challenge, we report the adaptation and use of an optimized tetra-cysteine minihelix both as a fusion protein and as a standalone reporter with the FlAsH dye. The fluorescent reporter helix is short enough to be encoded on a primer pair to tag any protein of interest via PCR. Both the tagged protein and the standalone reporter can be detected quantitatively in real time or at the end of cell-free expression reactions with standard 96/384-well plate readers, an RT-qPCR system, or gel electrophoresis without the need for staining. The fluorescent signal is stable and correlates linearly with the protein concentration, enabling product quantification. We modified the reporter to study cell-free expression dynamics and engineered ribosome activity. We anticipate that the fluorescent minihelix reporter will facilitate efforts in engineering in vitro transcription and translation systems.

Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists

Synthetic biology allows us to reuse, repurpose, and reconfigure biological systems to address society's most pressing challenges. Developing biotechnologies in this way requires integrating concepts across disciplines, posing challenges to educating students with diverse expertise. We created a framework for synthetic biology training that deconstructs biotechnologies across scales-molecular, circuit/network, cell/cell-free systems, biological communities, and societal-giving students a holistic toolkit to integrate cross-disciplinary concepts towards responsible innovation of successful biotechnologies. We present this framework, lessons learned, and inclusive teaching materials to allow its adaption to train the next generation of synthetic biologists.

Ribosome Pool Engineering Increases Protein Biosynthesis Yields

The biosynthetic capability of the bacterial ribosome motivates efforts to understand and harness sequence-optimized versions for synthetic biology. However, functional differences between natively occurring ribosomal RNA (rRNA) operon sequences remain poorly characterized. Here, we use an in vitro ribosome synthesis and translation platform to measure protein production capabilities of ribosomes derived from all unique combinations of 16S and 23S rRNAs from seven distinct Escherichia coli rRNA operon sequences. We observe that polymorphisms that distinguish native E. coli rRNA operons lead to significant functional changes in the resulting ribosomes, ranging from negligible or low gene expression to matching the protein production activity of the standard rRNA operon B sequence. We go on to generate strains expressing single rRNA operons and show that not only do some purified in vivo expressed homogeneous ribosome pools outperform the wild-type, heterogeneous ribosome pool but also that a crude cell lysate made from the strain expressing only operon A ribosomes shows significant yield increases for a panel of medically and industrially relevant proteins. We anticipate that ribosome pool engineering can be applied as a tool to increase yields across many protein biomanufacturing systems, as well as improve basic understanding of ribosome heterogeneity and evolution.

Validation of Cell-Free Protein Synthesis Aboard the International Space Station

Cell-free protein synthesis (CFPS) is a rapidly maturing in vitro gene expression platform that can be used to transcribe and translate nucleic acids at the point of need, enabling on-demand synthesis of peptide-based vaccines and biotherapeutics as well as the development of diagnostic tests for environmental contaminants and infectious agents. Unlike traditional cell-based systems, CFPS platforms do not require the maintenance of living cells and can be deployed with minimal equipment; therefore, they hold promise for applications in low-resource contexts, including spaceflight. Here, we evaluate the performance of the cell-free platform BioBits aboard the International Space Station by expressing RNA-based aptamers and fluorescent proteins that can serve as biological indicators. We validate two classes of biological sensors that detect either the small-molecule DFHBI or a specific RNA sequence. Upon detection of their respective analytes, both biological sensors produce fluorescent readouts that are visually confirmed using a hand-held fluorescence viewer and imaged for quantitative analysis. Our findings provide insights into the kinetics of cell-free transcription and translation in a microgravity environment and reveal that both biosensors perform robustly in space. Our findings lay the groundwork for portable, low-cost applications ranging from point-of-care health monitoring to on-demand detection of environmental hazards in low-resource communities both on Earth and beyond.