Engineered luciferase reporter from a deep sea shrimp utilizing a novel imidazopyrazinone substrate

Design of NanoBiT-Nanobody-based FGL1 biosensors for early assisted diagnosis of esophageal cancer

Esophageal cancer (EC) is one of the most common causes of cancer-related mortality due in part to challenges in early diagnosis. Biomarker identification is crucial for improved early screening and treatment strategies for patients. Firstly, we employed serum proteomics techniques to screen for potential biomarkers in 15 early-stage EC patients and 5 healthy individuals. Among the differentially expressed proteins, FGL1 emerged as a promising candidate (AUC = 0.974) for early detection of EC. Subsequently, we developed NanoBiT-conjugated dual nanobodies (NBNB) sensors for robust and quantitative signal detection in fetal bovine serum (FBS) in 30 min or less, with a limit of detection (LoD) of 11.38 pM. In a case-control study recruiting 96 EC patients and 99 control samples, testing serum samples with the developed NBNB sensors revealed significantly elevated serum level of FGL1 in all-stage EC patients (AUC = 0.7880) and early-stage EC patients (AUC = 0.8286). Additionally, the combined diagnostic performance of FGL1 and CEA in EC samples is notably enhanced (AUC = 0.8847). These findings propose FGL1 as a novel and promising target for the early-stage EC diagnosis and treatment selection. Furthermore, we applied the assay to patients across six types of cancer, suggesting FGL1 as a potential pan-cancer marker. This study introduces a rapid, easy-to-use, cost-effective, reliable, universal, and high-throughput alternative to meet the growing demand for cancer biomarker testing in both academic and clinical settings.

Collaborative light-off and light-on bacterial luciferase biosensors: Innovative approach for rapid contaminant detection

Bioluminescence-based light-off and light-on biosensors are widely used in environmental monitoring due to their rapid, cost-effective, real-time, and easy operation. However, stability and sensitivity issues in detecting real samples remain challenging. This study introduces a novel approach utilizing combined light-off and light-on biosensors for rapid and sensitive contaminants detection within 45 min in real samples. First, a recombinase-based state machine (RSM) was used to construct light-off RSM biosensors (light-off RSMs) for continuously strong light emission and overexpressing of outer membrane porins OmpC and OmpF enhanced their sensitivity to toxic contaminants. Additionally, a new experimental protocol containing the cell culture, collection, preparation, and the contaminant measurement was established for bioluminescent light-on whole-cell biosensors (light-on WCBs) in contaminant detection, initially developed using cadmium (Cd) and later applied to lead (Pb) and mercury (Hg). For Cd light-on WCBs, overexpressing OmpC and knocking out the contaminant exporter ZntA enhanced the accumulation of intracellular Cd in WCB cells, resulting in increased sensitivity to low concentrations of contaminants. Further, metabolic modifications in light-on WCBs significantly boosted luminescence. These genetic modified bacterial strains, whether freshly harvested or as freeze-dried powders, showed rapid luminescent responses to contaminants in the picomolar (pM) to nanomolar (nM) range within 45 min. Finally, the combined use of light-off RSMs and light-on WCBs successfully assessed toxicity and detected specific contaminants in real environmental and food samples. These strategies could be applied to developing other bacterial luciferase-based biosensors and even other types such as colorimetric biosensors.

Ratiometric bioluminescent detection of Cu(II) ion based on differences in enzymatic reaction kinetics of two luciferase variants

Heavy metal contamination in water bodies has raised global concerns due to its significant threats to both public health and ecosystem. Copper (Cu), one of the most widely used metals, is also an essential trace element in physiological systems. Excessive intake of Cu from water can cause toxicity, potentially resulting in serious health risks. Ensuring water safety necessitates the critical detection of copper ion (Cu2+). Here, we report a ratiometric bioluminescent detection method for Cu2+, DERK-Cu(II), which is based on the Distinct Enzymatic Reaction Kinetics of two luciferase variants. In DERK-Cu(II), the blue luminescent luciferase exhibits lower catalytic efficiency than the green luminescent luciferase, thus it is less inhibited by Cu2+. Consequently, the luminescence color of their mixture is dependent on the Cu2+ concentrations, enabling us to find an optimal mixing ratio at which luminescence color changes evidently from green to blue. Building on this, we established a quantitative detection method for Cu2+ using a smartphone and successfully measured the Cu2+ concentrations in several water samples. The method we developed, using the difference in reaction kinetics of two enzymes with the same substrate specificity, would become a versatile approach applicable to the development of other enzyme-based indicators.

Intravital Optical Bioimaging of Ovarian Cancer Using a Luminescent Cell Line

Intravital bioimaging based on luminescence is an important method for the development and testing of antitumor drugs on model animals and is an essential part of preclinical studies. Bioimaging based on luminescent systems, compared with fluorescent bioimaging, provides a high signal-to-noise ratio, which justifies the development of cell lines that stably express luciferase genes for their subsequent use in model animals. In this work, we describe the creation of a stable cell line SKOV3.ip1-NanoLuc constitutively expressing the NanoLuc luciferase gene. The developed cell line was shown to be effective for intravital luminescence bioimaging of immunodeficient animals with deep-seated intraperitoneal tumors, which can be considered as a model of late-stage ovarian cancer.

A general assay platform to study protein pharmacology using ligand-dependent structural dynamics

Drug design strategies represent a fundamental challenge in chemical biology that could benefit from the development of next-generation high-throughput assays. Here we demonstrate that structural dynamic changes induced by ligand binding can be transmitted to a sensor protein fused to a target protein terminus. Here, NanoLuc luciferase, used as the intact protein or its α-complementation peptide, was fused to seven proteins from distinct enzyme superfamilies resulting in sensitive ligand-dependent bioluminescent outputs. This finding allows a general non-competitive, function-independent, quantitative, isothermal gain-of-signal ligand binding readout. As applied to chemical library high throughput screening, we can observe multivariate pharmacologic outputs including cofactor-induced synergy in ligand binding, as well as an example of allosteric site binding. The structural dynamics response assay format described here can enable the investigation of proteins precluded from study due to cost-prohibitive, insensitive, or technically challenging assays, including from cell lysates containing endogenously expressed gene edited proteins.

Enzyme miniaturization: Revolutionizing future biocatalysts

Enzyme miniaturization offers a transformative approach to overcome limitations posed by the large size of conventional enzymes in industrial, therapeutic, and diagnostic applications. However, the evolutionary optimization of enzymes for activity and stability has not inherently favored compact structures, creating challenges for modern applications requiring smaller and more efficient catalysts. In this review, we surveyed the advantages of miniature enzymes, including enhanced expressivity, folding efficiency, thermostability, and resistance to proteolysis. We described the applications of miniature enzymes as biosensors, therapeutic agents, and industrial catalysts. We highlighted strategies such as genome mining, rational design, random deletion, and de novo design for achieving enzyme miniaturization, integrating both computational and experimental techniques. By investigating these approaches, we aim to provide a framework for advancing enzyme engineering, emphasizing the unique potential of smaller enzymes to revolutionize biocatalysis, gene therapy, and biosensing technologies.

Real-time bioluminescence imaging of nitroreductase in breast cancer bone metastasis

Bone metastasis is a leading cause of mortality in breast cancer patients. Monitoring biomarkers for bone metastasis in breast cancer is crucial for the development of effective interventional treatments. Despite being a highly vascularized tissue, the bone presents a particularly hypoxic environment. Tumor hypoxia is closely linked to increased levels of various reductases, including nitroreductase (NTR). Currently, there are few probes available to detect NTR levels in breast cancer bone metastases. Although bioluminescent imaging is promising due to its specificity and high signal-to-noise ratio, many probes face challenges such as short emission wavelengths, reliance on complex conditions like external adenosine triphosphate, or lack of tissue specificity. In this study, through "caging" the luciferase substrate with an NTR-responsive aromatic nitro recognition group, we developed a highly sensitive and selective NTR-sensitive bioluminescent probe. The resulting probe effectively detects NTR in breast cancer cells and enables real-time monitoring of NTR in a mouse model of breast cancer bone metastasis. Additionally, it can differentiate between primary and bone tumors, and allow continuous monitoring of NTR levels, thus providing valuable insights into bone tumor progression. This work provides a powerful tool for further understanding the biological functions of NTR in breast cancer bone metastasis.

Luciferase complementation for cellular assays beyond protein-protein interactions

Luciferase complementation assays have emerged in 2001 as a useful tool to analyze biological processes through diverse biological assays such as cellular studies and in vivo imaging. The assay has an advantage of wide dynamic ranges, high signal-to-noise ratios, and capability for real-time monitoring of dynamic biological events with a readout of bioluminescence. While it was initially harnessed for detecting protein-protein interactions, biosensors based on luciferase-fragment complementation have achieved significant advancements in their designs, expanding versatility and applicability beyond the initial scope. This review aims to provide a comprehensive overview of designing strategies employed in split luciferase complementation assays and to highlight their diverse bioanalytical applications. Because simple bi-molecular detection of protein-protein interactions by this approach is well-established, this review will focus on introducing diverse sensor designs using the concept of split luciferase complementation.

Protein Engineering for Spatiotemporally Resolved Cellular Monitoring

Protein engineering has been extensively applied to the development of genetically encoded reporters for spatiotemporally resolved monitoring of dynamic biochemical activity across cellular compartments in living cells. Genetically encoded reporters facilitate the visualization and recording of cellular processes, including transmission of signaling molecules, protease activity, and protein-protein interactions. In this review, we describe and assess common reporter motifs and protein engineering strategies for designing genetically encoded reporters. We also discuss essential parameters for evaluating genetically encoded reporters, along with future protein engineering opportunities in this field.

An optimized luciferin formulation for NanoLuc-based in vivo bioluminescence imaging

Bioluminescence imaging (BLI) is widely used in preclinical biomedical research for noninvasive tracking of cell populations and biochemical events in vivo. With recent improvements in BLI brightness from the engineering of bioluminescent enzymes (luciferases) and substrates (luciferins), optimizing luciferin formulations to maximize delivery and minimize toxicity becomes important, especially for marine coelenterazine-type luciferins with limited solubility. Here, we complete the characterization of a previously reported NanoLuc substrate, designated cephalofurimazine-9 (CFz9), and optimize its formulation with water-soluble excipients. We report a pH-controlled formulation of CFz9 enabling high-dose delivery to achieve peak brightness comparable to other furimazine analogs both inside and outside the brain while reducing toxicity. Thus, an optimized CFz9 formulation improves the performance and tolerability of whole-animal BLI with NanoLuc-based reporters.

Remote Silyl Groups Enhance Hydrolytic Stability and Photocleavage Efficiency in Carbamates for Protein Release

Photocleavable molecules are valuable tools for biological studies, enabling spatiotemporal activation of molecular functions within cellular environments. In particular, coumarin-based photolytic molecules are useful because of their ability to flexibly tune the wavelength of photostimulation through their structural modifications. Ideal photocleavable molecular tools require hydrolytic stability and selective susceptibility to photo stimuli. However, conventional coumarin-based molecules have not simultaneously achieved both highly efficient photocleavage and hydrolysis resistance. Herein, we proposed a novel molecular design concept that introduces a silyl group into coumarin-based molecules at a position remote from the photolabile bond, creating an ideal photocleavable molecule for chemical biology tools. The established orbital effect of the remotely introduced silyl group improves the photolysis efficiency of coumarin-based molecules, while its bulkiness substantially enhances their hydrolytic stability in aqueous environments and under enzymatic conditions. Furthermore, this improvement in molecular functionality contributes to the development of high-performance protein-release biomaterials.

Genetically-encoded temperature indicators for thermal biology

Temperature crucially affects molecular processes in living organisms and thus it is one of the vital physical parameters for life. To investigate how temperature is biologically maintained and regulated and its biological impact on organisms, it is essential to measure the spatial distribution and/or temporal changes of temperature across different biological scales, from whole organism to subcellular structures. Fluorescent nanothermometers have been developed as probes for temperature measurement by fluorescence microscopy for applications in microscopic scales where macroscopic temperature sensors are inaccessible, such as embryos, tissues, cells, and organelles. Although fluorescent nanothermometers have been developed from various materials, fluorescent protein-based ones are especially of interest because they can be introduced into cells as the transgenes for expression with or without specific localization, making them suitable for less-invasive temperature observation in living biological samples. In this article, we review protein-based fluorescent nanothermometers also known as genetically-encoded temperature indicators (GETIs), covering most published GETIs, for developers, users, and researchers in thermal biology as well as interested readers. We provide overviews of the temperature sensing mechanisms and measurement methods of these protein-based fluorescent nanothermometers. We then outline key information for GETI development, focusing on unique protein engineering techniques and building blocks distinct to GETIs, unlike other fluorescent nanothermometers. Furthermore, we propose several standards for the characterization of GETIs. Additionally, we explore various issues and offer perspectives in the field of thermal biology.

Detection of a large antigen through the masking and exposure of a fragment of split luciferase

We developed PMBiT, an antibody-binding Protein M (PM)-based bioluminescent probe that detects large antigens via luciferase reconstitution by exposing a luciferase fragment. Detection is achieved by exploiting the principle that the antibody, large antigen, and PM cannot form a complex simultaneously. PMBiT was prepared by conjugating PM with a HiBiT-based peptide from split NanoLuc luciferase through an Azide-DBCO click reaction. It retained its binding activity to the antibody and showed bioluminescence upon reconstitution of the luciferase with LgBiT, the other fragment of the split NanoLuc. Mixing PMBiT with various IgG antibodies resulted in decreased bioluminescence. In contrast, when PMBiT was mixed with IgG bound to its large antigen, such as human C-reactive protein, a dose-dependent increase in bioluminescence was obtained. Molecular dynamics simulations of PM showed that two regions in the C-terminus contribute to steric clashes with antigens owing to their relatively rigid structures. Furthermore, in silico analysis of the structure suggested that the antigen size was the primary factor blocking the binding of PMBiT to IgG for antigen detection. An immunoassay utilizing PMBiT does not require genetic manipulation of antibodies, allowing for seamless and scalable antibody replacement, and will advance the future of on-site detection and rapid diagnostics.

Bioluminescence readout lateral flow immunoassay using nanobody targeting aflatoxin B1

Multiple signal detection methods are known for lateral flow immunoassays (LFIAs), with colorimetric approaches dominating the field. However, their limited sensitivity is a remaining challenge. Fluorescence-based signaling is regarded as a more sensitive method, but it comes at the cost of partial sacrifice of the user-friendliness of LFIAs due to the requirement of an excitation light source. In this context, bioluminescence providing an inherently high signal to noise ratio without the need of excitation light could be an attractive alternative. But only a few studies have demonstrated the application of bioluminescence signaling in LFIAs. This work aimed at the development of a simple bioluminescence-based LFIA for the detection of aflatoxin B1 (AFB1), used as a model target in a competitive LFIA format. Signal transduction was achieved by nanobody-nanoluciferase (Nluc) fusion proteins. These small-sized recombinant heavy-chain-only antibodies derived from the camelidae family directly linked with the Nluc enzyme produce high intensity glow-type bioluminescence in combination with the furimazine substrate. LFIA devices consisting of a sample pad, nitrocellulose membrane and absorbent pad with AFB1-BSA conjugate deposited at the test line on the nitrocellulose membrane, achieved an LOD of 0.26 ng mL-1 for aqueous AFB1 solutions pre-mixed with Nanobody-Nluc and bioluminescence emission observed on an imaging system. More user-friendly LFIA devices with integrated conjugate pad and pre-deposited Nanobody-Nluc provided clear AFB1 concentration-dependent bioluminescence signals with low background and enabled readout with a standard digital camera, resulting in an LOD of 1.12 ng mL-1. Finally, the LFIA strips have been applied in AFB1-spiked oat milk samples. The LOD of 4.09 ng mL-1 achieved in the real sample matrix is well below the maximum allowable residual concentration of AFB1 in the U.S. (20 ng mL-1).

An updated review on the role of small molecules in mediating protein degradation

Targeted protein degradation (TPD) technologies, inspired by physiological processes, have recently provided new directions for drug development. Unlike conventional drug development focusing on targeting the active sites of disease-related proteins, TPD can utilize any nook or cranny of a protein to drive degradation through the cell's inherent destruction mechanism. It offers various advantages such as stronger pharmacological effects, an expanded range of drug targets, and higher selectivity. Based on the ubiquitin-proteasome system and the lysosomal degradation pathway, a variety of TPD strategies have been developed including PROTAC, PROTAB, and AUTOTAC. These TPD strategies have continuously enriched the toolbox for targeted protein degradation and expanded the scope of application, providing new ideas for biological research and drug discovery. This review attempts to introduce up-to-date research progress in the TPD strategies, focusing mainly on their design concepts, advantages, potential applications, and challenges, which may provide some inspiration for drug design, drug discovery, and clinical application for biologists and chemists.

An Msp1-Protease Chimera Captures Transient AAA+ Interactions and Unveils Ost4 Mislocalization Errors

Membrane protein homeostasis (proteostasis) is essential for maintaining the integrity of eukaryotic organelles. Msp1 is a membrane anchored AAA+ (ATPase Associated with cellular Activities) protein that maintains mitochondrial proteostasis by extracting aberrant proteins from the outer mitochondrial membrane. A comprehensive understanding of the physiological roles of Msp1 has been hindered because AAA+ proteins interact with substrates transiently and common strategies to stabilize this interaction lead to undesirable mitochondrial phenotypes. To circumvent these drawbacks, we fused catalytically active Msp1 to the inactivated protease domain of the AAA+ protease Yme1. The resulting chimera sequesters substrates in the catalytically inactive degradation chamber formed by the protease domain. We performed mass spectrometry analysis with the Msp1-protease chimera and identified the signal anchored protein Ost4 as a novel Msp1 substrate. Topology experiments show that Ost4 adopts mixed orientations when mislocalized to mitochondria and that Msp1 extracts mislocalized Ost4 regardless of orientation. Together, this work develops new tools for capturing transient interactions with AAA+ proteins, identifies new Msp1 substrates, and shows a surprising error in targeting of Ost4.

A suite of pre-assembled, pET28b-based Golden Gate vectors for efficient protein engineering and expression

Expression and purification of recombinant proteins in Escherichia coli is a bedrock technique in biochemistry and molecular biology. Expression optimization requires testing different combinations of solubility tags, affinity purification techniques, and site-specific proteases. This optimization is laborious and time-consuming as these features are spread across different vector series and require different cloning strategies with varying efficiencies. Modular cloning kits based on the Golden Gate system exist, but they are not optimized for protein biochemistry and are overly complicated for many applications, such as undergraduate research or simple screening of protein purification features. An ideal solution is for a single gene synthesis or PCR product to be compatible with a large series of pre-assembled Golden Gate vectors containing a broad array of purification features at either the N or C terminus. To our knowledge, no such system exists. To fulfill this unmet need, we Golden Gate domesticated the pET28b vector and developed a suite of 21 vectors with different combinations of purification tags, solubility domains, visualization/labeling tags, and protease sites. We also developed a vector series with nine different N-terminal tags and no C-terminal cloning scar. The system is modular, allowing users to easily customize the vectors with their preferred combinations of features. To allow for easy visual screening of cloned vectors, we optimized constitutive expression of the fluorescent protein mScarlet3 in the reverse strand, resulting in a red to white color change upon successful cloning. Testing with the model protein sfGFP shows the ease of visual screening, high efficiency of cloning, and robust protein expression. These vectors provide versatile, high-throughput solutions for protein engineering and functional studies in E. coli.

Involvement of Toxoplasma gondii natural antisense transcripts in cellular stress responses

Natural antisense transcripts (NATs), as a major subset of long non-coding RNAs (lncRNAs), are derived from every chromosome of Toxoplasma gondii, with the highest occurrence from ChrIa (18.4 NATs per Mbp) and the lowest from ChrIX (3.9 NATs per Mbp). GO analysis indicates that genes, which mRNA-NAT pairs are derived, are important for house-keeping and essential activities of T. gondii. Approximately half of protein encoding genes, whose loci also generate NATs, are involved in biological processes of metabolic processes and protein biochemistry and have canonical catalytic or binding activities. Using NAT of ubiquitin-like protease 1 (TgUlp1-NAT) as our study model, we showed that TgUlp1-NAT expression is part of cellular stress responses. Using a nanoluc reporter system, we confirmed that electroporation or membrane destabilization significantly induced TgUlp1-NAT expression. When the extracellular parasites were exposed to media containing high potassium, high sodium or altered osmotic pressure, TgUlp1-NAT expression was significantly down-regulated. In addition, two TgUlp1-NAT variants were detected in stressed T. gondii. One is an intron-retained variant, and the other is a spliced variant, referred to as TgUlp1-NATa and TgUlp1-NATb, respectively. The intronic sequence is 368 nts long, where regulatory small ncRNAs were derived. Taken together, we have confirmed that NAT expressions and functions are involved in cellular adaptation that allows T. gondii recover from stresses.

Optimized electroporation for efficient evaluation of genetic elements in Dichomitus squalens

Dichomitus squalens, a promising white-rot basidiomycete for industrial enzyme production, necessitates efficient genetic manipulation systems to fully leverage its biotechnological potential. Although established methods such as protoplast-mediated and Agrobacterium tumefaciens-mediated transformations are effective in D. squalens, they are complex and time-consuming. This study introduces the electroporation transformation system for D. squalens, which is simpler and timesaving. By optimizing electroporation parameters, we obtained 77 ± 11 transformants per μg of DNA. Furthermore, we validated the suitability of the Nourseothricin N-acetyl transferase gene as a selectable marker and the NanoLuciferase gene as a bioluminescent reporter in D. squalens using our refined electroporation protocol. This study expands the toolkit for genetic engineering in D. squalens, offering greater flexibility for future molecular investigations. The development of this electroporation system not only enhances the ease of genetic manipulation in D. squalens but also provides a foundation for further exploration of its enzymatic capabilities and potential applications in biotechnology. The streamlined protocol allows for more efficient and rapid genetic engineering, facilitating the study of gene function and the development of improved strains for industrial purposes.

One Tracer, Dual Platforms: Unlocking Versatility of Fluorescent Probes in TR-FRET and NanoBRET Target Engagement Assays

Target engagement assays are critical for drug discovery, with Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) and Nano Bioluminescence Resonance Energy Transfer (NanoBRET) representing two complementary approaches for biochemical and cellular evaluation. Traditionally, these platforms demand distinct fluorescent tracers tailored to their unique detection systems, requiring separate probe development for comprehensive target characterization. Despite their widespread adoption, the development of platform-specific fluorescent tracers often leads to increased costs and experimental complexity. In this study, two fluorescent tracers, T2- BODIPY -FL and T2-BODIPY-589, initially developed for receptor-interacting protein kinase 1 (RIPK1) target engagement studies in TR-FRET and NanoBRET applications respectively, were systematically evaluated for their performance across both platforms under various detection parameters. By evaluating their performance across both assay systems, we demonstrate that both tracers can effectively bridge biochemical and cellular assays, delivering reliable measurements. T2-BODIPY-589, with its red-shifted spectral properties, exhibits superior performance in NanoBRET assays (Z' up to 0.80) while maintaining acceptable functionality in TR-FRET systems (Z'=0.53). In contrast, T2-BODIPY -FL provides optimal performance for TR-FRET (Z'=0.57) but also demonstrates potential for use in NanoBRET (Z' up to 0.72), albeit with reduced efficiency. Competition assays with an unlabeled inhibitor yielded consistent binding constants across all tracer-platform combinations, validating their reliability for quantitative measurements. Our findings highlight the potential for integrating a single tracer across diverse assay platforms, reducing the need for separate probe development and enhancing experimental consistency. This approach has broad implications for streamlining assay development, improving data comparability, and enables more direct comparisons between biochemical and cellular data, with broader implications for integrated drug discovery programs across diverse target classes.

BODIPY-coelenterazine conjugates as self-illuminating substrates for NanoLuc

We report how the conjugation of coelenterazine (CTZ) to BODIPY retains its activity as a versatile substrate for luciferase-type enzymes opening the possibility of taking advantage of BODIPY's fluorescent properties and capacity to generate singlet oxygen. Bioluminescence imaging-guided photodynamic therapy or 1O2-triggered drug release are potential applications of these conjugates.

Simultaneous Detection of Multiple Analytes at Ambient Temperature Using Eukaryotic Artificial Cells with Modular and Robust Synthetic Riboswitches

Cell-free systems, which can express an easily detectable output (protein) with a DNA or mRNA template, are promising as foundations of biosensors devoid of cellular constraints. Moreover, by encasing them in membranes such as natural cells to create artificial cells, these systems can avoid the adverse effects of environmental inhibitory molecules. However, the bacterial systems generally used for this purpose do not function well at ambient temperatures. We here encapsulated a eukaryotic cell-free system consisting of wheat germ extract (WGE) and a DNA template encoding an analyte-responsive regulatory RNA (called a riboswitch) into giant unilamellar vesicles (GUVs) to create eukaryotic artificial cell-based sensors that function well at ambient temperature. First, we improved our previously reported eukaryotic synthetic riboswitches and WGE for use in GUVs by chimerizing two internal ribosome entry sites and optimizing magnesium concentrations, respectively, both of which increased the expression efficiency in GUVs several fold. Then, a DNA template encoding one of these riboswitches followed by a reporter protein was encapsulated with the optimized GUV-friendly WGE. Importantly, our previously established versatile method allowed for the rational design of highly efficient eukaryotic riboswitches that are responsive to a user-defined analyte. In fact, we utilized this method to successfully create three types of artificial cells, each of which responded to a specific, membrane-permeable analyte with wide-range, analyte-dose dependency and high sensitivity at ambient temperature. Finally, due to their orthogonality and robustness, we were able to mix a cocktail of these artificial cells to achieve simultaneous detection of the three analytes without significant barriers.

Development of a Highly Selective NanoBRET Probe to Assess MAGL Inhibition in Live Cells

Cell-free enzymatic assays are highly useful tools in early compound profiling due to their robustness and scalability. However, their inadequacy to reflect the complexity of target engagement in a cellular environment may lead to a significantly divergent pharmacology that is eventually observed in cells. The discrepancy that emerges from properties like permeability and unspecific protein binding may largely mislead lead compound selection to undergo further chemical optimization. We report the development of a new intracellular NanoBRET assay to assess MAGL inhibition in live cells. Based on a reverse design approach, a highly potent, reversible preclinical inhibitor was conjugated to the cell-permeable BODIPY590 acceptor fluorophore while retaining its overall balanced properties. An engineered MAGL-nanoluciferase (Nluc) fusion protein provided a suitable donor counterpart for the facile interrogation of intracellular ligand activity. Validation of assay conditions using a selection of known MAGL inhibitors set the stage for the evaluation of over 1'900 MAGL drug candidates derived from our discovery program. This evaluation enabled us to select compounds for further development based not only on target engagement, but also on favorable physicochemical parameters like permeability and protein binding. This study highlights the advantages of cell-based target engagement assays for accelerating compound profiling and progress at the early stages of drug discovery programs.

Nanobody-Based Immunoassays for the Detection of Food Hazards-A Review

Food safety remains a significant global challenge that affects human health. Various hazards, including microbiological and chemical threats, can compromise food safety throughout the supply chain. To address food safety issues and ensure public health, it is necessary to adopt rapid, accurate, and highly specific detection methods. Immunoassays are considered to be an effective method for the detection of highly sensitive biochemical indicators and provide an efficient platform for the identification of food hazards. In immunoassays, antibodies function as the primary recognition elements. Nanobodies have significant potential as valuable biomolecules in diagnostic applications. Their distinctive physicochemical and structural characteristics make them excellent candidates for the development of reliable diagnostic assays, and as promising alternatives to monoclonal and polyclonal antibodies. Herein, we summarize a comprehensive overview of the status and prospects of nanobody-based immunoassays in ensuring food safety. First, we begin with a historical perspective on the development of nanobodies and their unique characteristics. Subsequently, we explore the definitions and boundaries of immunoassays and immunosensors, before discussing the potential applications of nanobody-based immunoassays in food safety testing that have emerged over the past five years, and follow the different immunoassays, highlighting their advantages over traditional detection methods. Finally, the directions and challenges of nanobody-based immunoassays in food safety are discussed. Due to their remarkable sensitivity, specificity and versatility, nanobody-based immunoassays hold great promise in revolutionizing food safety testing and ensuring public health and well-being.

Neutrophil recruitment during intestinal inflammation primes Salmonella elimination by commensal E. coli in a context-dependent manner

Foodborne bacterial diarrhea involves complex pathogen-microbiota-host interactions. Pathogen-displacing probiotics are increasingly popular, but heterogeneous patient outcomes highlighted the need to understand individualized host-probiotic activity. Using the mouse gut commensal Escherichia coli 8178 and the human probiotic E. coli Nissle 1917, we found that the degree of protection against the enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm) varies across mice with distinct gut microbiotas. Pathogen clearance is linked to enteropathy severity and subsequent recruitment of intraluminal neutrophils, which differs in a microbiota-dependent manner. By combining mouse knockout and antibody-mediated depletion models with bacterial genetics, we show that neutrophils and host-derived reactive oxygen species directly influence E. coli-mediated S. Tm displacement by potentiating siderophore-bound toxin killing. Our work demonstrates how host immune factors shape pathogen-displacing probiotic efficiency while also revealing an unconventional antagonistic interaction where a gut commensal and the host synergize to displace an enteric pathogen.

Coelenterazine Analogs for Bioassays and Molecular Imaging

Coelenterazine (CTZ) is a common substrate of marine luciferases upon emission of bioluminescence (BL) in living organisms. Because CTZ works as a "luminophore" in the process of BL emission, the chemical modification has been centered for improving the optical properties of BL. In this review, we showcase recent advances in CTZ designs with unique functionalities. We first elucidate the light-emitting mechanisms of CTZ, and then focus on how the rational modification of CTZ analogs developed in recent years are connected to the development of unique functionalities even without luciferases, which include color tunability covering the visible region, specificity to various proteins (e.g., luciferase, albumin, and virus protein), and activatability to ions or reactive oxygen species (ROS) and anticancer drugs. This review provides new insights into the broad utilities of CTZ analogs with designed functionalities in bioassays and molecular imaging.

Rapid screening of primary and rationally synthesized anti-mycobacterial compounds in macrophage using double recombinant M. bovis BCG strain

Antimycobacterial screening is done primarily at three levels; in vitro, ex vivo and in vivo. In earlier studies, we had generated a double recombinant Mycobacterium bovis BCG strain carrying firefly and Renilla luciferase genes as two reporters under the control of a constitutive and an inducible mycobacterial promoter. The presence of dual reporters allows simultaneous expression and analysis of two reporter enzymes within a single system. The expression profile of the firefly luciferase gene, rendered by a constitutive mycobacterial promoter, corroborates with the decline in bacterial growth in response to a wide range of antimycobacterial drugs, while the enhanced expression of Renilla luciferase mirrors the selective induction of the reporter gene expression as a result of FAS-II pathway-specific inhibition. Thus, the double recombinant strain allows the screening of both primary and rationally synthesized FAS-II pathway inhibitors in a single assay. While this was successfully used for in vitro screening, ex vivo adaptation of this screen-system posed several challenges. The constitutive hsp60pr showed appreciable expression inside macrophages, but the expression of the inducible kas operon promoter was found to be meager. This became a limiting factor as more number of bacilli needed per screening sample and with continued treatment the decline in CFU level worsens the detection limit of the luciferase assay. To develop a screen-system that compensate the lower level expression of a given mycobacterial promoter inside macrophages we introduced Nano luciferase reporter in recombinant mycobacteria. Nano luciferase emits several-fold brighter luminescence than firefly and Renilla luciferases and duly compensates the lower level expression of the kas operon promoter inside macrophages. The newly engineered double recombinant strain stays stable inside macrophages and serves as a model screen-system for general and pathway specific anti-mycobacterial ex vivo screening. The turnaround time is significantly reduced and the outcomes are similar and more consistent with those attained using conventional CFU based procedures.

Light-chain split luciferase assay implicates pathological NOTCH3 thiol reactivity in inherited cerebral small vessel disease

Stereotyped mutations in NOTCH3 drive CADASIL, the leading inherited cause of stroke and vascular dementia. The vast majority of these mutations result in alterations in the number of cysteines in the gene product. However, non-cysteine-altering pathogenic mutations have also been identified, making it challenging to discriminate pathogenic from benign NOTCH3 sequence variants. Here, we present a method for quantitative assessment of NOTCH3 mutants, the light chain split luciferase (LSL) assay. In LSL, NOTCH3 mutant fragments, cloned between a split luciferase open reading frame, are transfected into cells, producing secreted luciferase activity that is dependent on the normal structure of NOTCH3. Insertion of point mutants that cause CADASIL results in significantly lower activity. Using a panel of 47 sequences, we determined the sensitivity and specificity of LSL for pathogenic NOTCH3 mutation discrimination to be 100% and 93%. LSL was also modestly successful in differentiating pathogenic proteins responsible for Marfan's disease and Stiff Skin Syndrome. Two additional parameters from the LSL analysis (TCEP rescue of activity and secretion index) were also shown to be useful in characterizing NOTCH3 mutants. We show that the spacing and primary sequence of the light chain module is an important component of the LSL assay, as a single light chain cysteine is critical for pathogenic sequence discrimination. Furthermore, we show that the activity of CADASIL mutant reporters is amplified by the application of cysteine-reactive iodoacetamide, suggesting that LSL may be deployed to screen for novel compounds that suppress pathogenic conformations of NOTCH3.

Regulation of nucleus-encoded trans-acting factors allows orthogonal fine-tuning of multiple transgenes in the chloroplast of Chlamydomonas reinhardtii

The green microalga Chlamydomonas reinhardtii is a promising host organism for the production of valuable compounds. Engineering the Chlamydomonas chloroplast genome offers several advantages over the nuclear genome, including targeted gene insertion, lack of silencing mechanisms, potentially higher protein production due to multiple genome copies and natural substrate abundance for metabolic engineering. Tuneable expression systems can be used to minimize competition between heterologous production and host cell viability. However, complex gene regulation and a lack of tight regulatory elements make this a challenge in the Chlamydomonas chloroplast. In this work, we develop two synthetic tuneable systems to control the expression of genes on the chloroplast genome, taking advantage of the properties of the vitamin B12-responsive METE promoter and a modified thiamine (vitamin B1) riboswitch, along with nucleus-encoded chloroplast-targeted regulatory proteins NAC2 and MRL1. We demonstrate the capacity of these systems for robust, fine-tuned control of several chloroplast transgenes, by addition of nanomolar levels of vitamins. The two systems have been combined in a single strain engineered to avoid effects on photosynthesis and are orthogonal to each other. They were then used to manipulate the production of an industrially relevant diterpenoid, casbene, by introducing and tuning expression of the coding sequence for casbene synthase, as well as regulating the metabolite flux towards casbene precursors, highlighting the utility of these systems for informing metabolic engineering approaches.

A Fluorescent Probe Enables the Discovery of Improved Antagonists Targeting the Intracellular Allosteric Site of the Chemokine Receptor CCR7

Intracellular ligands of G protein-coupled receptors (GPCRs) are gaining significant interest in drug discovery. Here, we report the development of the fluorescent ligand Mz437 (4) targeting the CC chemokine receptor CCR7 at an intracellular allosteric site. We demonstrate its experimental power by applying 4 to identify two improved intracellular CCR7 antagonists, SLW131 (10) and SLW132 (21m), developed by converting two weakly active antagonists into single- or double-digit nanomolar ligands with minimal modifications. The thiadiazoledioxide 10 was derived from the CCR7 antagonist Cmp2105 by removing a methyl group from the benzamide moiety, while the squaramide 21m was obtained from the CXCR1/CXCR2 antagonist and clinical candidate navarixin by replacing the ethyl substituent by a tert-butyl group to engage a lipophilic subpocket. We show that 10 and 21m qualify to probe CCR7 biology in recombinant and primary immune cells and expect our novel probes to facilitate the design of next-generation intracellular CCR7 ligands.

A Bioluminescent Probe for H2S Detection in Tumor Microenvironment

Hydrogen sulfide (H2S) is an endogenous gaseous signaling molecule that regulates various physiological functions, and its abnormal levels have been closely linked to the onset and progression of numerous diseases including renal cell carcinoma (RCC). RCC is the most common malignant tumor of the kidney, accounting for 85-90% of all kidney cancer cases. However, studies using H2S as a biomarker for monitoring RCC progression at the molecular level remain relatively limited. Most current H2S luminescent probes suffer from low sensitivity and often need external stimuli, such as cysteine, to artificially elevate H2S levels, thereby reducing their effectiveness in detecting H2S in cells or in vivo. Although bioluminescent imaging probes are gaining attention for their specificity and high signal-to-noise ratio, no existing probes are specifically designed for detecting H2S in RCC. Additionally, many bioluminescent probes face challenges such as short emission wavelengths or dependence on complex conditions such as external adenosine triphosphate (ATP). Herein, through "caging" the luciferin substrate QTZ with H2S recognition groups, a H2S-sensitive bioluminescent probe QTZ-N3 with good sensitivity (∼0.19 μM) and selectivity was prepared. QTZ-N3 can effectively detect endogenous H2S in 786-O-Nluc renal cancer cells and sensitively monitor H2S levels in the RCC xenograft nude mouse model without requiring stimuli like cysteine. Furthermore, QTZ-N3 allows for the real-time monitoring of H2S during tumor progression. This work lays a solid foundation for future understanding of the biological functions of H2S in vivo.

Internal cap-initiated translation for efficient protein production from circular mRNA

Circular mRNA faces challenges in enhancing its translation potential as an RNA therapeutic. Here we introduce two molecular designs that bolster circular mRNA translation through an internal cap-initiated mechanism. The first consists of a circular mRNA with a covalently attached N7-methylguanosine (m7G) cap through a branching structure (cap-circ mRNA). This modification allows circular mRNA to recruit translation machinery and produce proteins more efficiently than internal ribosome entry site (IRES)-containing circular mRNAs. Combining with an N1-methylpseudouridine (m1Ψ) modification, cap-circ mRNA exhibits a lower acute immunostimulatory effect, maintaining high translation in mice. The second design features the non-covalent attachment of an m7G cap to a circular mRNA through hybridization with an m7G cap-containing oligonucleotide, enhancing translation by more than 50-fold. This setup allows circular mRNAs to synthesize reporter proteins upon hybridizing with capped mRNAs or long non-coding RNAs and to undergo rolling circle-type translation. These advancements broaden the therapeutic applications of circular mRNAs by minimizing their molecular size, elevating translation efficiency and facilitating cell-type-selective translation.

Electrically Driven, Bioluminescent Compliant Devices for Soft Robotics

Soft robotics, a research field wherein robots are fabricated from compliant materials, has sparked widespread research interest because of its potential applications in a variety of scenarios. In soft robots, luminescence is an important functionality for communication and information transmission, and it is typically achieved through electroluminescence, which relies on synthetic substances activated by external electric sources, such as batteries. This paper focuses on the use of luciferase, a biologically derived luminescent enzyme, as a luminescent material. Bioluminescence, which is triggered by the luciferin-luciferase reaction, is highly energy-efficient, nontoxic, and eco-friendly. In this regard, a mammalian cell-derived secreted luciferase bioluminescent liquid was developed. This bioluminescent liquid is strongly bright, stable, freezable, and scalable for use as a soft robotic material. To investigate the applicability of this bioluminescent liquid to soft robotics, it was incorporated as an electrode in electrically driven soft actuators, sensors, and robots. Specifically, dielectric elastomer sensors (DESs) and dielectric elastomer actuators (DEAs) were fabricated and characterized using established fabrication processes. The resistivity of the bioluminescent liquid was found to be 448.1 Ω·cm. When the DES was subjected to uniaxial strain, it exhibited a linear response and large deformation of up to 200% strain, with a simultaneous luminance change of 27%. The DEA displayed an areal strain of 46.0% and a luminance change of 31% at an applied voltage of 3.4 kV. The waterproof bending DEA generated a tip angle of 21.8° at 10 kV and was applied to a jellyfish robot that could swim in water at a speed of 2.1 mm/s. The experimental results demonstrated the successful operation of these devices, validating the concept of energy-efficient, safe, and environmentally friendly bioluminescent soft robots.

Pharmacodynamics of Akt drugs revealed by a kinase-modulated bioluminescent indicator

Measuring pharmacodynamics (PD)-the biochemical effects of drug dosing-and correlating them with therapeutic efficacy in animal models is crucial for the development of effective drugs but traditional PD studies are labor and resource intensive. Here we developed a kinase-modulated bioluminescent indicator (KiMBI) for rapid, noninvasive PD assessment of Akt-targeted drugs, minimizing drug and animal use. Using KiMBI, we performed a structure-PD relationship analysis on the brain-active Akt inhibitor ipatasertib by generating and characterizing two novel analogs. One analog, ML-B01, successfully inhibited Akt in both the brain and the body. Interestingly, capivasertib, ipatasertib and ML-B01 all exhibited PD durations beyond their pharmacokinetic profiles. Furthermore, KiMBI revealed that the PD effects of an Akt-targeted proteolysis-targeting chimera degrader endured for over 3 days. Thus, bioluminescence imaging with Akt KiMBI provides a noninvasive and efficient method for in vivo visualization of the PD of Akt inhibitors and degraders.

Enhanced nanobody-driven bioluminescent immunoassay for rapid parathion detection using engineered split-nanoluciferase

In this work, with parathion, a typical forbidden organophosphate pesticide as target drug, an enhanced nanobody-driven bioluminescent immunoassay based on the engineered split-nanoluciferase (NanoLuc) was proposed. Concretely, through labeling 11S and β10, two split-NanoLuc units onto the anti-parathion nanobody (Nb) VHH9 and the artificial antigen H1 coupled with carrier protein ovalbumin (H1-OVA) respectively, an NanoLuc Binary Technology (NanoBiT) system was firstly developed in the form of homogeneous immunoassay, in which the luminescence signal was produced by the reassembled NanoLuc after the combination of the 11S-fused VHH9 and β10-labeled H1-OVA. Subsequently, in order to enhance the signal-to-noise (S/N) ratio, a novel strategy of splitting 11S into two smaller subunits Δ11S and β9 was adopted so then an NanoLuc Ternary Technology (NanoTeT) system based on tri-part components of β9-fused VHH9, β10-labeled H1-OVA and Δ11S was successfully established. The results showed that the maximum half inhibition concentration (IC50) for parathion can be as low as 2.04 ng/mL, 3.2-fold and 4.2-fold improved than that of the NanoBiT system and indirect competitive enzyme-linked immunosorbent assay (ic-ELISA). Meanwhile, the detection range was from 0.19 ng/mL to 22.11 ng/mL. More importantly, this method required simply a one-step incubation with all reagents mixed together, and the total time used in detection was only 10 min, 7-fold faster than ic-ELISA. Finally, the average recoveries for vegetable samples were from 84.8% to 122% with the coefficient of variance (CV) below 15%. Overall, this study provides a new platform for homogeneous immunoassay of the small-molecule contaminants.

A split intein and split luciferase-coupled system for detecting protein-protein interactions

Elucidation of protein-protein interactions (PPIs) represents one of the most important methods in biomedical research. Recently, PPIs have started to be exploited for drug discovery purposes and have thus attracted much attention from both the academic and pharmaceutical sectors. We previously developed a sensitive method, Split Intein-Mediated Protein Ligation (SIMPL), for detecting binary PPIs via irreversible splicing of the interacting proteins being investigated. Here, we incorporated tripart nanoluciferase (tNLuc) into the system, providing a luminescence signal which, in conjunction with homogenous liquid phase operation, improves the quantifiability and operability of the assay. Using a reference PPI set, we demonstrated an improvement in both sensitivity and specificity over the original SIMPL assay. Moreover, we designed the new SIMPL-tNLuc ('SIMPL2') platform with an inherent modularity allowing for flexible measurement of molecular modulators of target PPIs, including inhibitors, molecular glues and PROTACs. Our results demonstrate that SIMPL2 is a sensitive, cost- and labor-effective tool suitable for high-throughput screening (HTS) in both PPI mapping and drug discovery applications.

Novel replication-competent reporter-expressing Rift Valley fever viruses for molecular studies

Rift Valley fever virus (RVFV) is a mosquito-borne zoonotic disease that causes severe disease in both domestic and wild ungulates and humans, making it a significant threat to livestock and public health. The RVFV genome consists of three single-stranded, negative-sense RNA segments differing in size: small (S), medium (M), and large (L). Segment S encodes the virus nucleoprotein N and the virulence-associated factor non-structural (NSs) protein in opposite orientations, separated by an intergenic region (IGR). To overcome the current need to use secondary techniques to detect the presence of RVFV in infected cells, we used T7-driven polymerase plasmid-based reverse genetics to generate replication-competent recombinant (r)RVFV expressing Nanoluciferase (Nluc) or Venus fluorescent proteins. These reporter genes were used as valid surrogates to track the presence of RVFV in mammalian and insect cells. Notably, we explored the genome plasticity of RVFV and compared four different strategies by modifying the viral segment S to introduce the reporter gene foreign sequences. The reporter-expressing rRVFV were stable and able to replicate in cultured mammalian and insect cells, although to a lesser extent than the recombinant wild-type (WT) counterpart. Moreover, rRVFV-expressing reporter genes were validated to identify neutralizing antibodies or compounds with antiviral activity. In vivo, all mice infected with the reporter-expressing rRVFV displayed an attenuated phenotype, although at different levels. These rRVFV-expressing reporter genes provide a novel approach to better understand the biology and pathogenesis of RVFV and represent an excellent biotechnological tool for developing new therapeutics against RVFV infections.

IMPORTANCE

Rift Valley fever virus (RVFV) is a mosquito-borne virus and zoonotic agent threat that can be deadly to domestic or wild ungulates, and humans. In this work, we used reverse genetics approaches to explore the genome plasticity of RVFV by generating a set of recombinant (r)RVFV that express fluorescent or luminescent proteins to track viral infection. All the generated reporter-expressing rRVFVs were able to propagate in mammalian or insect cells and a mouse model of infection. Our studies may contribute to advances in research on RVFV and other bunyaviruses and pave the way for the development of novel vaccines and the identification of new antivirals for the prophylactic and therapeutic treatment, respectively, of RVFV infections.

Functional analysis of Candida albicans Cdr1 through homologous and heterologous expression studies

Candida albicans Cdr1 is a plasma membrane ATP-binding cassette transporter encoded by CDR1 that was first cloned 30 years ago in Saccharomyces cerevisiae. Increased expression of Cdr1 in C. albicans clinical isolates results in resistance to azole antifungals due to drug efflux from the cells. Knowledge of Cdr1 structure and function could enable the design of Cdr1 inhibitors that overcome efflux-mediated drug resistance. This article reviews the use of expression systems to study Cdr1. Since the discovery of CDR1 in 1995, 123 studies have investigated Cdr1 using either heterologous or homologous expression systems. The majority of studies have employed integrative transformation and expression in S. cerevisiae. We describe a suite of plasmids with a range of useful protein tags for integrative transformation that enable the creation of tandem-gene arrays stably integrated into the S. cerevisiae genome, and a model for Cdr1 transport function. While expression in S. cerevisiae generates a strong phenotype and high yields of Cdr1, it is a nonnative environment and may result in altered structure and function. Membrane lipid composition and architecture affects membrane protein function and a focus on homologous expression in C. albicans may permit a more accurate understanding of Cdr1 structure and function.

Development of a highly sensitive method to detect translational infidelity

Protein homeostasis (proteostasis) is the balance of protein synthesis, protein maintenance, and degradation. Loss of proteostasis contributes to the aging process and characterizes neurodegenerative diseases. It is well established that the processes of protein maintenance and degradation are declining with aging; however, the contribution of a declining quality of protein synthesis to the loss of proteostasis is less well understood. In fact, protein synthesis at the ribosome is an error-prone process and challenges the cell with misfolded proteins. Here, we present the development of a highly sensitive and reproducible reporter assay for the detection of translational errors and the measurement of translational fidelity. Using Nano-luciferase, an enzyme 3 times smaller and 50 times more sensitive than the hitherto used Firefly-luciferase, we introduced stop-codon and amino-acid exchanges that inactivate the enzyme. Erroneous re-activation of luciferase activity indicates ribosomal inaccuracy and translational infidelity. This highly sensitive and reproducible method has broad applications for studying the molecular mechanisms underlying diseases associated with defective protein synthesis and can be used for drug screening to modulate translational fidelity.

The short conserved region-2 of LARP4 interacts with ribosome-associated RACK1 and promotes translation

LARP4 interacts with poly(A)-binding protein (PABP) to protect messenger RNAs (mRNAs) from deadenylation and decay, and recent data indicate it can direct the translation of functionally related mRNA subsets. LARP4 was known to bind RACK1, a ribosome-associated protein, although the specific regions involved and relevance had been undetermined. Here, through a combination of in-cell and in vitro methodologies, we identified positions 615-625 in conserved region-2 (CR2) of LARP4 (and 646-656 in LARP4B) as directly binding RACK1. Consistent with these results, AlphaFold2-Multimer predicted high-confidence interaction of CR2 with RACK1 propellers 5 and 6. CR2 mutations strongly decreased LARP4 association with cellular RACK1 and ribosomes by multiple assays, whereas PABP association was less affected, consistent with independent interactions. The CR2 mutations decreased LARP4's ability to stabilize a β-globin mRNA reporter containing an AU-rich element (ARE) to higher degree than β-globin and GFP (green fluorescent protein) mRNAs lacking the ARE. We show LARP4 robustly increases translation of β-glo-ARE mRNA, whereas the LARP4 CR2 mutant is impaired. Analysis of nanoLuc-ARE mRNA for production of luciferase activity confirmed LARP4 promotes translation efficiency, while CR2 mutations are disabling. Thus, LARP4 CR2-mediated interaction with RACK1 can promote translational efficiency of some mRNAs.

Creating coveted bioluminescence colors for simultaneous multi-color bioimaging

Bioluminescence, an optical marker that does not require excitation by light, allows researchers to simultaneously observe multiple targets, each exhibiting a different color. Notably, the colors of the bioluminescent proteins must sufficiently vary to enable simultaneous detection. Here, we aimed to introduce a method that can be used to expand the color variation by tuning dual-acceptor bioluminescence resonance energy transfer. Using this approach, we could visualize multiple targets with up to 20 colors through single-shot acquisition using a color complementary metal-oxide semiconductor camera. Overall, this method enables simple and simultaneous observation of multiple biological targets and phenomena.

Engineering Phages to Fight Multidrug-Resistant Bacteria

Facing the global "superbug" crisis due to the emergence and selection for antibiotic resistance, phages are among the most promising solutions. Fighting multidrug-resistant bacteria requires precise diagnosis of bacterial pathogens and specific cell-killing. Phages have several potential advantages over conventional antibacterial agents such as host specificity, self-amplification, easy production, low toxicity as well as biofilm degradation. However, the narrow host range, uncharacterized properties, as well as potential risks from exponential replication and evolution of natural phages, currently limit their applications. Engineering phages can not only enhance the host bacteria range and improve phage efficacy, but also confer new functions. This review first summarizes major phage engineering techniques including both chemical modification and genetic engineering. Subsequent sections discuss the applications of engineered phages for bacterial pathogen detection and ablation through interdisciplinary approaches of synthetic biology and nanotechnology. We discuss future directions and persistent challenges in the ongoing exploration of phage engineering for pathogen control.

PEGylated ATP-Independent Luciferins for Noninvasive High-Sensitivity High-Speed Bioluminescence Imaging

Bioluminescence imaging (BLI) is a powerful, noninvasive imaging method for animal studies. NanoLuc luciferase and its derivatives are attractive bioluminescent reporters recognized for their efficient photon production and ATP independence. However, utilizing them for animal imaging poses notable challenges. Low substrate solubility has been a prominent problem, limiting in vivo brightness, while the susceptibility of luciferins to auto-oxidation by molecular oxygen in air increases handling complexity and poses an obstacle to obtaining consistent results. To address these issues, we developed a range of caged PEGylated luciferins with increased auto-oxidation resistance and water solubility of up to 25 mM, resulting in substantial in vivo bioluminescence increases in mouse models. This advancement has created the brightest and most sensitive luciferase-luciferin combination, enabling high-speed video-rate imaging of freely moving mice with brain-expressed luciferase. These innovative substrates offer new possibilities for investigating a wide range of biological processes and are poised to become invaluable resources for chemical, biological, and biomedical fields.

Best Practices and Pitfalls in Developing Nanomaterial Delivery Tools for Plants

Numerous reports of nanomaterial-assisted delivery of DNA, RNA, and protein to plants for biotechnology applications emerged over the past decade. While the field has experienced rapid growth, best practices for developing and validating nanomaterial delivery tools for plants have not yet been established. Best practices are well-established for clinical/animal cell delivery experiments, yet plants pose a distinct challenge requiring separate considerations due to their unique tissue structures and cellular morphology. In this Perspective, we provide recommendations and highlight pitfalls in developing nanomaterial tools for delivery of "Central Dogma" cargos to plants. Given the ongoing interest in the field, this discussion will aid in improving the rigor of this nascent field toward practical applications of nanomaterial delivery tools.

A suite of pre-assembled, pET28b-based Golden Gate vectors for efficient protein engineering and expression

Expression and purification of recombinant proteins in E. coli is a bedrock technique in biochemistry and molecular biology. Expression optimization requires testing different combinations of solubility tags, affinity purification techniques, and site-specific proteases. This optimization is laborious and time consuming as these features are spread across different vector series and require different cloning strategies with varying efficiencies. Modular cloning kits based on the Golden Gate system exist, but are overly complicated for many applications, such as undergraduate research or simple screening of protein purification features. An ideal solution is for a single gene synthesis or PCR product to be compatible with a large series of pre-assembled Golden Gate vectors containing a broad array of purification features at either the N or C-terminus. To our knowledge, no such system exists. To fulfill this unmet need, we Golden Gate domesticated the pET28b vector and developed a suite of 21 vectors with different combinations of purification tags, solubility domains, visualization/labeling tags, and protease sites. We also developed a completely scarless vector series with 9 different N-terminal tags. The system is modular, allowing users to easily customize the vectors with their preferred combinations of features. To allow for easy visual screening of cloned vectors, we optimized constitutive expression of the fluorescent protein mScarlet3 in the reverse strand, resulting in a red to white color change upon successful cloning. Testing with the model protein sfGFP shows the ease of visual screening, high efficiency of cloning, and robust protein expression. These vectors provide versatile, high-throughput solutions for protein engineering and functional studies in E. coli.

CaBLAM! A high-contrast bioluminescent Ca2+ indicator derived from an engineered Oplophorus gracilirostris luciferase

Ca2+ plays many critical roles in cell physiology and biochemistry, leading researchers to develop a number of fluorescent small molecule dyes and genetically encodable probes that optically report changes in Ca2+ concentrations in living cells. Though such fluorescence-based genetically encoded Ca2+ indicators (GECIs) have become a mainstay of modern Ca2+ sensing and imaging, bioluminescence-based GECIs-probes that generate light through oxidation of a small-molecule by a luciferase or photoprotein-have several distinct advantages over their fluorescent counterparts. Bioluminescent tags do not photobleach, do not suffer from nonspecific autofluorescent background, and do not lead to phototoxicity since they do not require the extremely bright extrinsic excitation light typically required for fluorescence imaging, especially with 2-photon microscopy. Current BL GECIs perform poorly relative to fluorescent GECIs, producing small changes in bioluminescence intensity due to high baseline signal at resting Ca2+ concentrations and suboptimal Ca2+ affinities. Here, we describe the development of a new bioluminescent GECI, "CaBLAM," which displays much higher contrast (dynamic range) than previously described bioluminescent GECIs and has a Ca2+ affinity suitable for capturing physiological changes in cytosolic Ca2+ concentration. Derived from a new variant of Oplophorus gracilirostris luciferase with superior in vitro properties and a highly favorable scaffold for insertion of sensor domains, CaBLAM allows for single-cell and subcellular resolution imaging of Ca2+ dynamics at high frame rates in cultured neurons and in vivo. CaBLAM marks a significant milestone in the GECI timeline, enabling Ca2+ recordings with high spatial and temporal resolution without perturbing cells with intense excitation light.

Luminescence-based complementation assay to assess target engagement and cell permeability of glycolate oxidase (HAO1) inhibitors

Glycolate oxidase (HAO1) catalyses the synthesis of glyoxylate, a common metabolic intermediate that causes renal failure if accumulated. HAO1 inhibition is an emerging treatment for primary hyperoxaluria, a rare disorder of glyoxylate metabolism. Here we report the first cell-based measurement of inhibitor uptake and engagement with HAO1, by adapting the cellular thermal shift assay (CETSA) based on Nano luciferase complementation and luminescence readout. By profiling the interaction between HAO1 and four well-characterised inhibitors in intact and lysed HEK293T cells, we showed that our CETSA method differentiates between low-permeability/high-engagement and high-permeability/low-engagement ligands and is able to rank HAO1 inhibitors in line with both recombinant protein methods and previously reported indirect cellular assays. Our methodology addresses the unmet need for a robust, sensitive, and scalable cellular assay to guide HAO1 inhibitor development and, in broader terms, can be rapidly adapted for other targets to simultaneously monitor compound affinity and cellular permeability.

A yeast-assembled, plasmid-launched reverse genetics system for the murine coronavirus MHV-A59

The Betacoronavirus murine hepatitis virus (MHV) is an important model system for studying coronavirus (CoV) molecular and cell biology. Despite this, few reagents for MHV are available through repositories such as ATCC or Addgene, potentially limiting the widespread adoption of MHV as a tractable model system. To overcome some challenges inherent in the existing MHV reverse genetics systems, we developed a plasmid-launched transformation-associated recombination (TAR) cloning-based system to assemble the MHV (strain A59; MHV-A59) genome. Following assembly in yeast, virus replication was launched by transfecting the fully assembled genome into HEK-293T cells. MHV-A59 recovered using this TAR cloning-based approach (WTTAR MHV-A59) replicated with kinetics identical to the virus recovered using a ligation- and T7-based approach (WTLIG MHV-A59). Additionally, WTTAR MHV-A59 can be detected at least 10 h post-transfection without requiring additional nucleocapsid (N) provided in trans. Lastly, we demonstrated the tractability of this TAR cloning-based system by recovering MHV-A59 expressing an 11 amino acid-containing HiBiT tag fused to the C-terminus of spike (S). While this virus, SC MHV-A59, replicated with reduced kinetics compared to WTTAR MHV-A59, the kinetics of virion production could be measured over time directly from the supernatant. This report represents the first plasmid-launched, TAR cloning-based system for MHV-A59. Furthermore, it describes a new reporter virus that could be used to study early steps during MHV-A59 entry and be used in the screening of antiviral compounds. To support future research with MHV-A59, we have made the necessary plasmids for this system available through ATCC.

Genetically encoded bioluminescent glucose indicator for biological research

Glucose is an essential energy source in living cells and is involved in various phenomena. To understand the roles of glucose, measuring cellular glucose levels is important. Here, we developed a bioluminescent glucose indicator called LOTUS-Glc. Unlike fluorescence, bioluminescence doesn't require excitation light when imaging. Using LOTUS-Glc, we demonstrated drug effect evaluation, concurrent use with the optogenetic tool in HEK293T cells, and the measurement of light-dependent glucose fluctuations in plant-derived protoplasts. LOTUS-Glc would be a useful tool for understanding the roles of glucose in living organisms.

Evaluation of Vaccinia Virus Infection in Mice Using Two-Reporter Recombinant Virus

The family Poxviridae comprises multiple viruses with large double-stranded (ds) DNA genomes that can infect numerous vertebrate and invertebrate hosts, including humans. The development of genetic engineering methods for Vaccinia virus (VACV), the prototypic member in the family, have allowed the manipulation of the genomes of poxviruses for the generation of recombinant (r)VACV expressing easily traceable luciferase and/or fluorescent reporter genes. These recombinant viruses have significantly contributed to progress in the field of poxvirus research and accelerated the development of novel prophylactic vaccines and therapeutic antiviral treatments. Recently, we described two reporter rVACV expressing luciferase (Nluc) and fluorescent (GFP or Scarlet) proteins to easily track viral infections in different systems, overcoming the limitations associated with the use of rVACV expressing a single luciferase or fluorescent reporter gene. Here, we describe the experimental procedures to carry out in vitro, in vivo and ex vivo studies using these novel bireporter-expressing rVACV, which also represent an excellent option to study the biology of VACV, including the use of these reporter viruses for testing new antivirals and vaccines, using cultured cells and/or well-characterized animal models of infection.