A Split Methyl Halide Transferase AND Gate That Reports by Synthesizing an Indicator Gas

Ribozyme-Mediated Gene-Fragment Complementation for Nondestructive Reporting of DNA Transfer within Soil

Enzymes that produce volatile metabolites can be coded into genetic circuits to report nondisruptively on microbial behaviors in hard-to-image soils. However, these enzyme reporters remain challenging to apply in gene transfer studies due to leaky off states that can lead to false positives. To overcome this problem, we designed a reporter that uses ribozyme-mediated gene-fragment complementation of a methyl halide transferase (MHT) to regulate the synthesis of methyl halide gases. We split the mht gene into two nonfunctional fragments and attached these to a pair of splicing ribozyme fragments. While the individual mht-ribozyme fragments did not produce methyl halides when transcribed alone in Escherichia coli, coexpression resulted in a spliced transcript that translated the MHT reporter. When cells containing one mht-ribozyme fragment transcribed from a mobile plasmid were mixed with cells that transcribed the second mht-ribozyme fragment, methyl halides were only detected following rare conjugation events. When conjugation was performed in soil, it led to a 16-fold increase in methyl halides in the soil headspace. These findings show how ribozyme-mediated gene-fragment complementation can achieve tight control of protein reporter production, a level of control that will be critical for monitoring the effects of soil conditions on gene transfer and the fidelity of biocontainment measures developed for environmental applications.

Synthetic microbiology in sustainability applications

Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.

Split Proteins and Reassembly Modules for Biological Applications

Split systems, modular entities enabling controlled biological processes, have become instrumental in biological research. This review highlights their utility across applications like gene regulation, protein interaction identification, and biosensor development. Covering significant progress over the last decade, it revisits traditional split proteins such as GFP, luciferase, and inteins, and explores advancements in technologies like Cas proteins and base editors. We also examine reassembly modules and their applications in diverse fields, from gene regulation to therapeutic innovation. This review offers a comprehensive perspective on the recent evolution of split systems in biological research.

Integration of multiple stress signals in plants using synthetic Boolean logic gates

As photosynthetic organisms, plants have a potential role in the sustainable production of high-value products such as medicines, biofuels, and chemical feedstocks. With effective engineering using synthetic biology approaches, plant-based platforms could conceivably be designed to minimize the costs and waste of production for materials that would otherwise be uneconomical. Additionally, modern agricultural crops could be engineered to be more productive, resilient, or restorative in different or rapidly changing environments and climates. Information-processing genetic devices and circuits containing multiple interacting parts that behave predictably must be developed to achieve these complex goals. A genetic Boolean AND logic gate is a device that computes the presence or absence of two inputs (signals, stimuli) and produces an output (response) only when both inputs are present. We optimized individual genetic components and used synthetic protein heterodimerizing domains to rationally assemble genetic AND logic gates that integrate two hormonal inputs in transgenic Arabidopsis thaliana plants. These AND gates produce an output only in the presence of both abscisic acid and auxin but not when either or neither hormone is present. The AND logic gate can also integrate signals resulting from two plant stresses, cold temperature and bacterial infection, to produce a response. The design principles used here are generalizable, and, therefore, multiple orthogonal AND gates could be assembled and rationally layered to process complex genetic information in plants. These layered logic gates may be used in genetic circuits to probe fundamental questions in plant biology, such as hormonal crosstalk, in addition to plant engineering for bioproduction.

A split ribozyme that links detection of a native RNA to orthogonal protein outputs

Individual RNA remains a challenging signal to synthetically transduce into different types of cellular information. Here, we describe Ribozyme-ENabled Detection of RNA (RENDR), a plug-and-play strategy that uses cellular transcripts to template the assembly of split ribozymes, triggering splicing reactions that generate orthogonal protein outputs. To identify split ribozymes that require templating for splicing, we use laboratory evolution to evaluate the activities of different split variants of the Tetrahymena thermophila ribozyme. The best design delivers a 93-fold dynamic range of splicing with RENDR controlling fluorescent protein production in response to an RNA input. We further resolve a thermodynamic model to guide RENDR design, show how input signals can be transduced into diverse outputs, demonstrate portability across different bacteria, and use RENDR to detect antibiotic-resistant bacteria. This work shows how transcriptional signals can be monitored in situ and converted into different types of biochemical information using RNA synthetic biology.

Genetic Circuit Design in Rhizobacteria

Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.

Strategies for Improving Small-Molecule Biosensors in Bacteria

In recent years, small-molecule biosensors have become increasingly important in synthetic biology and biochemistry, with numerous new applications continuing to be developed throughout the field. For many biosensors, however, their utility is hindered by poor functionality. Here, we review the known types of mechanisms of biosensors within bacterial cells, and the types of approaches for optimizing different biosensor functional parameters. Discussed approaches for improving biosensor functionality include methods of directly engineering biosensor genes, considerations for choosing genetic reporters, approaches for tuning gene expression, and strategies for incorporating additional genetic modules.

The challenges of monitoring and manipulating anaerobic microbial communities

Mixed anaerobic microbial communities are a key component in valorization of waste biomass via anaerobic digestion. Similar microbial communities are important as soil and animal microbiomes and have played a critical role in shaping the planet as it is today. Understanding how individual species within communities interact with others and their environment is important for improving performance and potential applications of an inherently green technology. Here, the challenges associated with making measurements critical to assessing the status of anaerobic microbial communities are considered. How these measurements could be incorporated into control philosophies and augment the potential of anaerobic microbial communities to produce different and higher value products from waste materials are discussed. The benefits and pitfalls of current genetic and molecular approaches to measuring and manipulating anaerobic microbial communities and the challenges which should be addressed to realise the potential of this exciting technology are explored.

Control of synthetic microbial consortia in time, space, and composition

While synthetic microbial systems are becoming increasingly complicated, single-strain systems cannot match the complexity of their multicellular counterparts. Such complexity, however, is much more difficult to control. Recent advances have increased our ability to control temporal, spatial, and community compositional organization, including modular adhesive systems, strain growth relationships, and asymmetric cell division. While these systems generally work independently, combining them into unified systems has proven difficult. Once such unification is proven successful we will unlock a new frontier of synthetic biology and open the door to the creation of synthetic biological systems with true multicellularity.

Rational engineering of a modular bacterial CRISPR-Cas activation platform with expanded target range

CRISPR-Cas activator (CRISPRa) systems that selectively turn on transcription of a target gene are a potentially transformative technology for programming cellular function. While in eukaryotes versatile CRISPRa systems exist, in bacteria these systems suffer from a limited ability to activate different genes due to strict distance-dependent requirements of functional target binding sites, and require greater customization to optimize performance in different genetic and cellular contexts. To address this, we apply a rational protein engineering approach to create a new CRISPRa platform that is highly modular to allow for easy customization and has increased targeting flexibility through harnessing engineered Cas proteins. We first demonstrate that transcription activation domains can be recruited by CRISPR-Cas through noncovalent protein-protein interactions, which allows each component to be encoded on separate and easily interchangeable plasmid elements. We then exploit this modularity to rapidly screen a library of different activation domains, creating new systems with distinct regulatory properties. Furthermore, we demonstrate that by harnessing a library of circularly permuted Cas proteins, we can create CRISPRa systems that have different target binding site requirements, which together, allow for expanded target range.

Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences

The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open questions, including understanding microbial behaviors in heterogeneous matrices like soils, sediments, and wastewater systems, tracking cryptic element cycling in the Earth system, and establishing the dynamics of microbe-microbe, microbe-plant, and microbe-material interactions. Before these new tools can reach their potential, however, a suite of biological parts and microbial chassis appropriate for environmental conditions must be developed by the synthetic biology community. This includes diversifying sensing modules to obtain information relevant to environmental questions, creating output signals that allow dynamic reporting from hard-to-image environmental materials, and tuning these sensors so that they reliably function long enough to be useful for environmental studies. Finally, ethical questions related to the use of synthetic biosensors in environmental applications are discussed.