An auxin-inducible, GAL4-compatible, gene expression system for Drosophila

Stage-specific modulation of Drosophila gene expression with muscle GAL4 promoters

The bipartite GAL4/UAS system is the most widely used method for targeted gene expression in Drosophila melanogaster and facilitates rapid in vivo genetic experimentation. Defining precise gene expression patterns for tissues and/or cell types under GAL4 control will continue to evolve to suit experimental needs. However, the precise spatial and temporal expression patterns for some commonly used muscle tissue promoters are still unclear. This missing information limits the precise timing of experiments during development. Here, we focus on three muscle-enriched GAL4 drivers (Mef2-GAL4, C57-GAL4 and G7-GAL4) to better inform selection of the most appropriate muscle promoter for experimental needs. Specifically, C57-GAL4 and G7-GAL4 turn on in the first or second instar larval stages, respectively, and can be used to bypass myogenesis for studies of muscle function after development.

Spatiotemporal control of cell ablation using Ronidazole with Nitroreductase in Drosophila

The ability to induce cell death in a controlled stereotypic manner has led to the discovery of evolutionary conserved molecules and signaling pathways necessary for tissue growth, repair, and regeneration. Here we report the development of a new method to genetically induce cell death in a controlled stereotypic manner in Drosophila. This method has advantages over other current methods and relies on expression of the E. coli enzyme Nitroreductase (NTR) with exogenous application of the nitroimidazole prodrug, Ronidazole. NTR expression is controlled spatially using the GAL4/UAS system while temporal control of cell death is achieved through timed feeding of Ronidazole supplied in the diet. In cells expressing NTR, Ronidazole is converted to a toxic substance inducing DNA damage and cell death. Caspase cell death is achieved in a range of NTR-expressing cell types with Ronidazole feeding, including epithelial, neurons, and glia. Removing Ronidazole from the diet restores cell death to normal unperturbed levels. Unlike other genetic ablation methods, temporal control is achieved through feeding not temperature, circumventing developmental complications associated with temperature changes. Ronidazole-NTR also requires only two transgenes, a GAL4 driver and UAS-NTR, which is generated as a GFP-NTR fusion allowing for easy setup of large-scale screening of UAS-RNAi lines. Altogether, Ronidazole-NTR provides a new streamlined method for inducing cell death in Drosophila with temperature-independent ON/OFF control.

Regulation of CAR transgene expression to design semiautonomous CAR-T

Effective transgene expression is critical for genetically engineered cell therapy. Therefore, one of CAR-T cell therapy's critical areas of interest, both in registered products and next-generation approaches is the expression of transgenes. It turns out that various constitutive promoters used in clinical products may influence CAR-T cell antitumor effectiveness and impact the manufacturing process. Furthermore, next-generation CAR-T starts to install remotely controlled inducible promoters or even autonomous expression systems, opening new ways of priming, boosting, and increasing the safety of CAR-T. In this article, a wide range of constitutive and inducible promoters has been grouped and structured, making it possible to compare their pros and cons as well as clinical usage. Finally, logic gates based on Synthetic Notch have been elaborated, demonstrating the coupling of desired external signals with genetically engineered cellular responses.

Diverting organic waste from landfills via insect biomanufacturing using engineered black soldier flies (Hermetia illucens)

A major roadblock towards the realisation of a circular economy are the lack of high-value products that can be generated from waste. Black soldier flies (BSF; Hermetia illucens) are gaining traction for their ability to rapidly consume large quantities of organic wastes. However, these are primarily used to produce a small variety of products, such as animal feed ingredients and fertiliser. Using synthetic biology, BSF could be developed into a novel sustainable biomanufacturing platform to valorise a broader variety of organic waste feedstocks into enhanced animal feeds, a large variety of high-value biomolecules including industrial enzymes and lipids, and improved fertiliser.

A subclass of evening cells promotes the switch from arousal to sleep at dusk

Animals exhibit rhythmic patterns of behavior that are shaped by an internal circadian clock and the external environment. Although light intensity varies across the day, there are particularly robust differences at twilight (dawn/dusk). These periods are also associated with major changes in behavioral states, such as the transition from arousal to sleep. However, the neural mechanisms by which time and environmental conditions promote these behavioral transitions are poorly defined. Here, we show that the E1 subclass of Drosophila evening clock neurons promotes the transition from arousal to sleep at dusk. We first demonstrate that the cell-autonomous clocks of E2 neurons primarily drive and adjust the phase of evening anticipation, the canonical behavior associated with "evening" clock neurons. We next show that conditionally silencing E1 neurons causes a significant delay in sleep onset after dusk. However, rather than simply promoting sleep, activating E1 neurons produces time- and light-dependent effects on behavior. Activation of E1 neurons has no effect early in the day but then triggers arousal before dusk and induces sleep after dusk. Strikingly, these activation-induced phenotypes depend on the presence of light during the day. Despite their influence on behavior around dusk, in vivo voltage imaging of E1 neurons reveals that their spiking rate and pattern do not significantly change throughout the day. Moreover, E1-specific clock ablation has no effect on arousal or sleep. Thus, we suggest that, rather than specifying "evening" time, E1 neurons act, in concert with other rhythmic neurons, to promote behavioral transitions at dusk.

Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals

At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.

A drug stabilizable GAL80ds for conditional control of gene expression via GAL4-UAS and CRISPR-Cas9 systems in Drosophila

The binary GAL4-UAS expression system has been widely used in Drosophila to achieve tissue-specific expression of genes. To further allow for simultaneous spatial and conditional control of gene expression in existing GAL4 expression lines backgrounds, temperature and chemical controllable GAL80 variants have been engineered. Here we add a new drug stabilizable GAL80ds variant, by fusing it to a low-background DHFR-22-DD. We first quantify both single (DD-GAL80) and double (DD-GAL80-DD) architectures and show varied background and activation levels. Next, we demonstrate the utility of GAL80ds Drosophila line to regulate a cell death gene ectopically, in a drug-dependent manner, by utilizing an existing tissue-specific GAL4 driver that regulates the expression of a cell death gene under a UAS. Finally, we showcase the usefulness of GAL80ds in tight drug-mediated regulation of a target gene, from an endogenous locus, by utilizing an existing tissue-specific GAL4 to drive the expression of a dead Cas9 variant fused to the transcriptional coactivator nejire, under a UAS and in gRNA lines. Overall, these new GAL80ds lines expand the use of the wide variety of existing tissue-specific GAL4 and gene-specific gRNA lines. This enables conditional control of genes, both ectopically and endogenously, for a broad array of gene expression control applications.

Arabidopsis as a model for translational research

Arabidopsis thaliana is currently the most-studied plant species on earth, with an unprecedented number of genetic, genomic, and molecular resources having been generated in this plant model. In the era of translating foundational discoveries to crops and beyond, we aimed to highlight the utility and challenges of using Arabidopsis as a reference for applied plant biology research, agricultural innovation, biotechnology, and medicine. We hope that this review will inspire the next generation of plant biologists to continue leveraging Arabidopsis as a robust and convenient experimental system to address fundamental and applied questions in biology. We aim to encourage lab and field scientists alike to take advantage of the vast Arabidopsis datasets, annotations, germplasm, constructs, methods, molecular and computational tools in our pursuit to advance understanding of plant biology and help feed the world's growing population. We envision that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability.

Auxin exposure disrupts feeding behavior and fatty acid metabolism in adult Drosophila

The ease of genetic manipulation in Drosophila melanogaster using the Gal4/UAS system has been beneficial in addressing key biological questions. Current modifications of this methodology to temporally induce transgene expression require temperature changes or exposure to exogenous compounds, both of which have been shown to have detrimental effects on physiological processes. The recently described auxin-inducible gene expression system (AGES) utilizes the plant hormone auxin to induce transgene expression and is proposed to be the least toxic compound for genetic manipulation, with no obvious effects on Drosophila development and survival in one wild-type strain. Here, we show that auxin delays larval development in another widely used fly strain, and that short- and long-term auxin exposure in adult Drosophila induces observable changes in physiology and feeding behavior. We further reveal a dosage response to adult survival upon auxin exposure, and that the recommended auxin concentration for AGES alters feeding activity. Furthermore, auxin-fed male and female flies exhibit a significant decrease in triglyceride levels and display altered transcription of fatty acid metabolism genes. Although fatty acid metabolism is disrupted, auxin does not significantly impact adult female fecundity or progeny survival, suggesting AGES may be an ideal methodology for studying limited biological processes. These results emphasize that experiments using temporal binary systems must be carefully designed and controlled to avoid confounding effects and misinterpretation of results.

A cGAL-UAS bipartite expression toolkit for Caenorhabditis elegans sensory neurons

Animals integrate sensory information from the environment and display various behaviors in response to external stimuli. In Caenorhabditis elegans hermaphrodites, 33 types of sensory neurons are responsible for chemosensation, olfaction, and mechanosensation. However, the functional roles of all sensory neurons have not been systematically studied due to the lack of facile genetic accessibility. A bipartite cGAL-UAS system has been previously developed to study tissue- or cell-specific functions in C. elegans. Here, we report a toolkit of new cGAL drivers that can facilitate the analysis of a vast majority of the 60 sensory neurons in C. elegans hermaphrodites. We generated 37 sensory neuronal cGAL drivers that drive cGAL expression by cell-specific regulatory sequences or intersection of two distinct regulatory regions with overlapping expression (split cGAL). Most cGAL-drivers exhibit expression in single types of cells. We also constructed 28 UAS effectors that allow expression of proteins to perturb or interrogate sensory neurons of choice. This cGAL-UAS sensory neuron toolkit provides a genetic platform to systematically study the functions of C. elegans sensory neurons.

Auxin Exposure Disrupts Feeding Behavior and Fatty Acid Metabolism in Adult Drosophila

The ease of genetic manipulation in Drosophila melanogaster using the Gal4/UAS system has been beneficial in addressing key biological questions. Current modifications of this methodology to temporally induce transgene expression require temperature changes or exposure to exogenous compounds, both of which have been shown to have detrimental effects on physiological processes. The recently described auxin-inducible gene expression system (AGES) utilizes the plant hormone auxin to induce transgene expression and is proposed to be the least toxic compound for genetic manipulation, with no obvious effects on Drosophila development and survival in one wild-type strain. Here we show that auxin delays larval development in another widely-used fly strain, and that short- and long-term auxin exposure in adult Drosophila induces observable changes in physiology and feeding behavior. We further reveal a dosage response to adult survival upon auxin exposure, and that the recommended auxin concentration for AGES alters feeding activity. Furthermore, auxin fed male and female flies exhibit a significant decrease in triglyceride levels and display altered transcription of fatty acid metabolism genes. Although fatty acid metabolism is disrupted, auxin does not significantly impact adult female fecundity or progeny survival, suggesting AGES may be an ideal methodology for studying limited biological processes. These results emphasize that experiments using temporal binary systems must be carefully designed and controlled to avoid confounding effects and misinterpretation of results.

Interactions between innate immunity and insulin signaling affect resistance to infection in insects

An active immune response is energetically demanding and requires reallocation of nutrients to support resistance to and tolerance of infection. Insulin signaling is a critical global regulator of metabolism and whole-body homeostasis in response to nutrient availability and energetic needs, including those required for mobilization of energy in support of the immune system. In this review, we share findings that demonstrate interactions between innate immune activity and insulin signaling primarily in the insect model Drosophila melanogaster as well as other insects like Bombyx mori and Anopheles mosquitos. These studies indicate that insulin signaling and innate immune activation have reciprocal effects on each other, but that those effects vary depending on the type of pathogen, route of infection, and nutritional status of the host. Future research will be required to further understand the detailed mechanisms by which innate immunity and insulin signaling activity impact each other.

Increase in brain glycogen levels ameliorates Huntington's disease phenotype and rescues neurodegeneration in Drosophila

Under normal physiological conditions, the mammalian brain contains very little glycogen, most of which is stored in astrocytes. However, the aging brain and the subareas of the brain in patients with neurodegenerative disorders tend to accumulate glycogen, the cause and significance of which remain largely unexplored. Using cellular models, we have recently demonstrated a neuroprotective role for neuronal glycogen and glycogen synthase in the context of Huntington's disease. To gain insight into the role of brain glycogen in regulating proteotoxicity, we utilized a Drosophila model of Huntington's disease, in which glycogen synthase is either knocked down or expressed ectopically. Enhancing glycogen synthesis in the brains of flies with Huntington's disease decreased mutant Huntingtin aggregation and reduced oxidative stress by activating auto-lysosomal functions. Further, overexpression of glycogen synthase in the brain rescues photoreceptor degeneration, improves locomotor deficits and increases fitness traits in this Huntington's disease model. We, thus, provide in vivo evidence for the neuroprotective functions of glycogen synthase and glycogen in neurodegenerative conditions, and their role in the neuronal autophagy process.

A subclass of evening cells promotes the switch from arousal to sleep at dusk

Animals exhibit rhythmic patterns of behavior that are shaped by an internal circadian clock and the external environment. While light intensity varies across the day, there are particularly robust differences at twilight (dawn/dusk). These periods are also associated with major changes in behavioral states, such as the transition from arousal to sleep. However, the neural mechanisms by which time and environmental conditions promote these behavioral transitions are poorly defined. Here, we show that the E1 subclass of Drosophila evening clock neurons promotes the transition from arousal to sleep at dusk. We first demonstrate that the cell-autonomous clocks of E2 neurons alone are required to drive and adjust the phase of evening anticipation, the canonical behavior associated with "evening" clock neurons. We next show that conditionally silencing E1 neurons causes a significant delay in sleep onset after dusk. However, rather than simply promoting sleep, activating E1 neurons produces time- and light- dependent effects on behavior. Activation of E1 neurons has no effect early in the day, but then triggers arousal before dusk and induces sleep after dusk. Strikingly, these phenotypes critically depend on the presence of light during the day. Despite their influence on behavior around dusk, in vivo voltage imaging of E1 neurons reveals that their spiking rate does not vary between dawn and dusk. Moreover, E1-specific clock ablation has no effect on arousal or sleep. Thus, we suggest that, rather than specifying "evening" time, E1 neurons act, in concert with other rhythmic neurons, to promote behavioral transitions at dusk.

Dissecting neuron-specific functions of circadian genes using modified cell-specific CRISPR approaches

Circadian behavioral rhythms in Drosophila melanogaster are regulated by about 75 pairs of brain neurons. They all express the core clock genes but have distinct functions and gene expression profiles. To understand the importance of these distinct molecular programs, neuron-specific gene manipulations are essential. Although RNAi based methods are standard to manipulate gene expression in a cell-specific manner, they are often ineffective, especially in assays involving smaller numbers of neurons or weaker Gal4 drivers. We and others recently exploited a neuron-specific CRISPR-based method to mutagenize genes within circadian neurons. Here, we further explore this approach to mutagenize three well-studied clock genes: the transcription factor gene vrille, the photoreceptor gene Cryptochrome (cry), and the neuropeptide gene Pdf (pigment dispersing factor). The CRISPR-based strategy not only reproduced their known phenotypes but also assigned cry function for different light-mediated phenotypes to discrete, different subsets of clock neurons. We further tested two recently published methods for temporal regulation in adult neurons, inducible Cas9 and the auxin-inducible gene expression system. The results were not identical, but both approaches successfully showed that the adult-specific knockout of the neuropeptide Pdf reproduces the canonical loss-of-function mutant phenotypes. In summary, a CRISPR-based strategy is a highly effective, reliable, and general method to temporally manipulate gene function in specific adult neurons.

An optimized temporally controlled Gal4 system in Drosophila reveals degeneration caused by adult-onset neuronal Vps13D knockdown

Mutations in the human gene VPS13D cause the adult-onset neurodegenerative disease ataxia. Our previous work showed that disruptions in the Vps13D gene in Drosophila neurons causes mitochondrial defects. However, developmental lethality caused by Vps13D loss limited our understanding of the long-term physiological effects of Vps13D perturbation in neurons. Here, we optimized a previously generated system to temporally knock down Vps13D expression precisely in adult Drosophila neurons using a modification to the Gal4/UAS system. Adult-onset activation of Gal4 was enacted using the chemically-inducible tool which fuses a destabilization-domain to the Gal4 repressor Gal80 (Gal80-DD). Optimization of the Gal80-DD tool shows that feeding animals the DD-stabilizing drug trimethoprim (TMP) during development and rearing at a reduced temperature maximally represses Gal4 activity. Temperature shift and removal of TMP from the food after eclosion robustly activates Gal4 expression in adult neurons. Using the optimized Gal80-DD system, we find that adult-onset Vps13D RNAi expression in neurons causes the accumulation of mitophagy intermediates, progressive deficits in locomotor activity, early lethality, and brain vacuolization characteristic of neurodegeneration. The development of this optimized system allows us to more precisely examine the degenerative phenotypes caused by Vps13D disruption, and can likely be utilized in the future for other genes associated with neurological diseases whose manipulation causes developmental lethality in Drosophila.

Comparison of neuronal GAL4 drivers along with the AGES (auxin-inducible gene expression system) and TARGET (temporal and regional gene expression targeting) systems for fine tuning of neuronal gene expression in Drosophila

Spatial and temporal control of gene expression in Drosophila is essential in elucidating gene function. Spatial control is facilitated by the UAS/GAL4 system, and this can be coupled with additional adaptations for precise temporal control and fine tuning of gene expression levels. Here we directly compare the level of pan-neuronal transgene expression governed by nSyb-GAL4 and elav-GAL4, as well as mushroom body-specific expression alongside OK107-GAL4. We also compare the temporal modulation of gene expression in neurons with the auxin-inducible gene expression system (AGES) and temporal and regional gene expression targeting (TARGET) systems.

Targeting endogenous proteins for spatial and temporal knockdown using auxin-inducible degron in Caenorhabditis elegans

The auxin-inducible degron (AID) provides reversible, spatiotemporal control for the knockdown of target proteins. Here, we present a protocol for AID-mediated protein knockdown in Caenorhabditis elegans. We describe steps for generating the knock-in mutants using two CRISPR-Cas9 genome editing techniques and preparing the auxin-containing nematode growth media (NGM) plates. We also detail AID-mediated spatiotemporal protein knockdown. For complete details on the use and execution of this protocol, please refer to Kurashina et al. (2021).1.

Analysis of Physiological Control of Adult Drosophila Oogenesis by Interorgan Communication

Tissue homeostasis is dependent on the interaction between various organs within an organism in response to physiological inputs. The adult Drosophila melanogaster ovary is sensitive to environmental challenges and has recently been shown to be regulated by signaling from peripheral organs. To dissect the intricate coordination between overall organism health and reproduction, it is necessary to meticulously characterize both experimental tools and oogenesis processes. This chapter provides a guide for the careful analysis of interorgan communication in regulating oogenesis in adult Drosophila melanogaster.

On the trail of auxin: Reporters and sensors

The phytohormone auxin is a master regulator of plant growth and development in response to many endogenous and environmental signals. The underlying coordination of growth is mediated by the formation of auxin maxima and concentration gradients. The visualization of auxin dynamics and distribution can therefore provide essential information to increase our understanding of the mechanisms by which auxin orchestrates these growth and developmental processes. Several auxin reporters have been developed to better perceive the auxin distribution and signaling machinery in vivo. This review focuses on different types of auxin reporters and biosensors used to monitor auxin distribution and its dynamics, as well as auxin signaling, at the cellular and tissue levels in different plant species. We provide a brief history of each reporter and biosensor group and explain their principles and utilities.