What's hot today: Current papers in developmental biology and gene function

What's hot today:
Current papers in developmental biology and gene function

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Monday, April 29th, 2025 - Adult neural development, structure, and function

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Delgado, R., Wilson, C. A. M., Caballero, L., Melo, F., Bacigalupo, J. (2024). Mechanical force activates the light-dependent channels TRP and TRPL in excised patches from the rhabdomere of Drosophila photoreceptors. Neuroscience, 555:23-31 PubMed ID: 39032804
Summary:
Drosophila phototransduction in light-sensitive microvilli involves a metabotropic signaling cascade. Photoisomerized rhodopsin couples to G-protein, activating phospholipase C, which cleaves phosphatidylinositol bisphosphate (PIP2) into inositol trisphosphate, diacylglycerol (DAG) and a proton. DAG is converted into phosphatidic acid by DAG-kinase and metabolized to L-linoleoyl glycerol (2-LG) by DAG-lipase. This complex enzyme cascade ultimately opens the light-dependent transient receptor potential channels, TRP and TRPL. PIP2, DAG, H(+) and 2-LG are possible channel activators, either individually or combined, but their direct participation in channel-gating remains unresolved. Molecular interaction with the channels, modification of the channels' lipid moiety and mechanical force on the channels by changes in the membrane structure derived from light-dependent changes in lipid composition are possible gating agents. In this regard, mechanical activation was suggested, based on a rapid light-dependent contraction of the photoreceptors mediated by the phototransduction cascade. This studying further examined this possibility by applying force to inside-out patches from the microvilli membrane by changing the pressure in the pipette or pulling the membrane with a magnet through superparamagnetic nanospheres. The channels were opened by mechanical force, while mutant lacking both channels was insensitive to mechanical stimulation. Atomic Force Microscopy showed that the stiffness of an artificial phospholipid bilayer was increased by arachidonic acid and diacylglycerol whereas elaidic acid was ineffective, mirroring their relative effects in channel activity previously observed electrophysiologically. Together, the results are consistent with the notion that light-induced changes in lipid composition alter the membrane structure, generating mechanical force on the channels leading to channel opening.

Nanami, T., Yamada, D., Someya, M., Hige, T., Kazama, H., Kohno, T. (2024). A lightweight data-driven spiking neuronal network model of Drosophila olfactory nervous system with dedicated hardware support. Frontiers in neuroscience, 18:1384336 PubMed ID: 38994271
Summary:
Data-driven spiking neuronal network (SNN) models enable in-silico analysis of the nervous system at the cellular and synaptic level. Therefore, they are a key tool for elucidating the information processing principles of the brain. While extensive research has focused on developing data-driven SNN models for mammalian brains, their complexity poses challenges in achieving precision. Network topology often relies on statistical inference, and the functions of specific brain regions and supporting neuronal activities remain unclear. Additionally, these models demand huge computing facilities and their simulation speed is considerably slower than real-time. This study proposes a lightweight data-driven SNN model that strikes a balance between simplicity and reproducibility. The model is built using a qualitative modeling approach that can reproduce key dynamics of neuronal activity. The Drosophila olfactory nervous system was targeted, extracting its network topology from connectome data. The model was successfully implemented on a small entry-level field-programmable gate array and simulated the activity of a network in real-time. In addition, the model reproduced olfactory associative learning, the primary function of the olfactory system, and characteristic spiking activities of different neuron types. In sum, this paper propose a method for building data-driven SNN models from biological data. This approach reproduces the function and neuronal activities of the nervous system and is lightweight, acceleratable with dedicated hardware, making it scalable to large-scale networks. Therefore, this approach is expected to play an important role in elucidating the brain's information processing at the cellular and synaptic level through an analysis-by-construction approach. In addition, it may be applicable to edge artificial intelligence systems in the future.

Leier, H. C., Foden, A. J., Jindal, D. A., Wilkov, A. J., Van der Linden Costello, P., Vanderzalm, P. J., Coutinho-Budd, J. C., Tabuchi, M., Broihier, H. T. (2024). Glia control experience-dependent plasticity in an olfactory critical period. bioRxiv, PubMed ID: 39005309
Summary:
Sensory experience during developmental critical periods has lifelong consequences for circuit function and behavior, but the molecular and cellular mechanisms through which experience causes these changes are not well understood. The Drosophila antennal lobe houses synapses between olfactory sensory neurons (OSNs) and downstream projection neurons (PNs) in stereotyped glomeruli. Many glomeruli exhibit structural plasticity in response to early-life odor exposure, indicating a general sensitivity of the fly olfactory circuitry to early sensory experience. Gliaz were recently found to regulate the development of the antennal lobe in young adult flies, leading the question of whether glia also drive experience-dependent plasticity. This study defines a critical period for structural and functional plasticity of OSN-PN synapses in the ethyl butyrate (EB)-sensitive glomerulus VM7. EB exposure for the first two days post-eclosion drives large-scale reductions in glomerular volume, presynapse number, and post-synaptic activity. The highly conserved engulfment receptor Draper is required for this critical period plasticity. Specifically, ensheathing glia upregulate Draper expression, invade the VM7 glomerulus, and phagocytose OSN presynaptic terminals in response to critical-period EB exposure. Crucially, synapse pruning during the critical period has long-term consequences for circuit function since both OSN-PN synapse number and spontaneous activity of PNs remain persistently decreased. These data demonstrate experience-dependent pruning of synapses in olfactory circuitry and argue that the Drosophila antennal lobe will be a powerful model for defining the function of glia in critical period plasticity.

Lacin, H., Zhu, Y., DiPaola, J. T., Wilson, B. A., Zhu, Y., Skeath, J. B. (2024). A genetic screen in Drosophila uncovers a role for senseless-2 in surface glia in the peripheral nervous system to regulate CNS morphology. G3 (Bethesda), 14(9) PubMed ID: 38996053
Summary:
Despite increasing in mass approximately 100-fold during larval life, the Drosophila CNS maintains its characteristic form. Dynamic interactions between the overlying basement membrane and underlying surface glia are known to regulate CNS structure in Drosophila, but the genes and pathways that establish and maintain CNS morphology during development remain poorly characterized. To identify genes that regulate CNS shape in Drosophila, an EMS-based, forward genetic screen was conducted of the second chromosome, uncovered 50 mutations that disrupt CNS structure, and mapped these alleles to 17 genes. Analysis of whole genome sequencing data wedded to genetic studies uncovered the affected gene for all but 1 mutation. Identified genes include well-characterized regulators of tissue shape, like LanB1, viking, and Collagen type IV alpha1, and previously characterized genes, such as Toll-2 and Rme-8, with no known role in regulating CNS structure. We also uncovered that papilin and C1GalTA"> likely act in the same pathway to regulate CNS structure: the fly homolog of a glucuronosyltransferase, B4GAT1/LARGE1, that regulates Dystroglycan function in mammals is required to maintain CNS shape in Drosophila. Finally, that the transcription factor senseless-2 was shown to expressed and functions specifically in surface glia found on peripheral nerves but not in the CNS to govern CNS structure, identifying a gene that functionally subdivides a glial subtype along the peripheral-central axis. Future work on these genes should clarify the genetic mechanisms that ensure the homeostasis of CNS form during development.

Poe, A. R., Zhu, L., Tang, S. H., Valencia, E., Kayser, M. S. (2024). Energetic demands regulate sleep-wake rhythm circuit development. Elife, 13 PubMed ID: 39037919
Summary:
Sleep and feeding patterns lack strong daily rhythms during early life. As diurnal animals mature, feeding is consolidated to the day and sleep to the night. In Drosophila, circadian sleep patterns are initiated with formation of a circuit connecting the central clock to arousal output neurons; emergence of circadian sleep also enables long-term memory (LTM). However, the cues that trigger the development of this clock-arousal circuit are unknown. This study identifed a role for nutritional status in driving sleep-wake rhythm development in Drosophila larvae. In the 2nd instar larval period (L2), sleep and feeding are spread across the day; these behaviors become organized into daily patterns by the 3rd instar larval stage (L3). Forcing mature (L3) animals to adopt immature (L2) feeding strategies disrupts sleep-wake rhythms and the ability to exhibit LTM. In addition, the development of the clock (DN1a)-arousal (Dh44) circuit itself is influenced by the larval nutritional environment. Finally, larval arousal Dh44 neurons were shown to act through glucose metabolic genes to drive onset of daily sleep-wake rhythms. Together, these data suggest that changes to energetic demands in developing organisms trigger the formation of sleep-circadian circuits and behaviors.

Ganguly, I., Heckman, E. L., Litwin-Kumar, A., Clowney, E. J., Behnia, R. (2024). Diversity of visual inputs to Kenyon cells of the Drosophila mushroom body. Nat Commun, 15(1):5698 PubMed ID: 38972924
Summary:
The arthropod mushroom body is well-studied as an expansion layer representing olfactory stimuli and linking them to contingent events. However, 8% of mushroom body Kenyon cells in Drosophila melanogaster receive predominantly visual input, and their function remains unclear. This study identified inputs to visual Kenyon cells using the FlyWire adult whole-brain connectome. Input repertoires are similar across hemispheres and connectomes with certain inputs highly overrepresented. Many visual neurons presynaptic to Kenyon cells have large receptive fields, while interneuron inputs receive spatially restricted signals that may be tuned to specific visual features. Individual visual Kenyon cells randomly sample sparse inputs from combinations of visual channels, including multiple optic lobe neuropils. These connectivity patterns suggest that visual coding in the mushroom body, like olfactory coding, is sparse, distributed, and combinatorial. However, the specific input repertoire to the smaller population of visual Kenyon cells suggests a constrained encoding of visual stimuli.

Thursday, April 25th, 2025 - Signaling

Lacin, H., Zhu, Y., DiPaola, J. T., Wilson, B. A., Zhu, Y., Skeath, J. B. (2024). A genetic screen in Drosophila uncovers a role for senseless-2 in surface glia in the peripheral nervous system to regulate CNS morphology. G3 (Bethesda), 14(9) PubMed ID: 38996053
Summary:
Despite increasing in mass approximately 100-fold during larval life, the Drosophila CNS maintains its characteristic form. Dynamic interactions between the overlying basement membrane and underlying surface glia are known to regulate CNS structure in Drosophila, but the genes and pathways that establish and maintain CNS morphology during development remain poorly characterized. To identify genes that regulate CNS shape in Drosophila, an EMS-based, forward genetic screen was conducted of the second chromosome, uncovered 50 mutations that disrupt CNS structure, and mapped these alleles to 17 genes. Analysis of whole genome sequencing data wedded to genetic studies uncovered the affected gene for all but 1 mutation. Identified genes include well-characterized regulators of tissue shape, like LanB1, viking, and Collagen type IV alpha1, and previously characterized genes, such as Toll-2 and Rme-8, with no known role in regulating CNS structure. We also uncovered that papilin and C1GalTA" likely act in the same pathway to regulate CNS structure: the fly homolog of a glucuronosyltransferase, B4GAT1/LARGE1, that regulates Dystroglycan function in mammals is required to maintain CNS shape in Drosophila. Finally, that the transcription factor senseless-2 was shown to expressed and functions specifically in surface glia found on peripheral nerves but not in the CNS to govern CNS structure, identifying a gene that functionally subdivides a glial subtype along the peripheral-central axis. Future work on these genes should clarify the genetic mechanisms that ensure the homeostasis of CNS form during development.

Thursday, April 25th, 2025 - Signaling

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Cupo, C., Allan, C., Ailiani, V., Kasza, K. E. (2024). Signatures of structural disorder in developing epithelial tissues. bioRxiv, PubMed ID: 38405955
Summary:
Epithelial cells generate functional tissues in developing embryos through collective movements and shape changes. In some morphogenetic events, a tissue dramatically reorganizes its internal structure - often generating high degrees of structural disorder - to accomplish changes in tissue shape. However, the origins of structural disorder in epithelia and what roles it might play in morphogenesis are poorly understood. This question was examined in the Drosophila germband epithelium, which undergoes dramatic changes in internal structure as cell rearrangements drive elongation of the embryo body axis. Using two order parameters that quantify volumetric and shear disorder, structural disorder was shown to increase during body axis elongation and is strongly linked with specific developmental processes. Both disorder metrics begin to increase around the onset of axis elongation, but then plateau at values that are maintained throughout the process. Notably, the disorder plateau values for volumetric disorder are similar to those for random cell packings, suggesting this may reflect a limit on tissue behavior. In mutant embryos with disrupted external stresses from the ventral furrow, both disorder metrics reach wild-type maximum disorder values with a delay, correlating with delays in cell rearrangements. In contrast, in mutants with disrupted internal stresses and cell rearrangements, volumetric disorder is reduced compared to wild type, whereas shear disorder depends on specific external stress patterns. Together, these findings demonstrate that internal and external stresses both contribute to epithelial tissue disorder and suggest that the maximum values of disorder in a developing tissue reflect physical or biological limits on morphogenesis.

Kodra, A. L., Singh, A. S., de la Cova, C., Ziosi, M., Johnston, L. A. (2024). The Drosophila tumor necrosis factor Eiger promotes Myc supercompetition independent of canonical Jun N-terminal kinase signaling. Genetics, 228(1) PubMed ID: 38985651
Summary:
Numerous factors have been implicated in the cell-cell interactions that lead to elimination of cells via cell competition, a context-dependent process of cell selection in somatic tissues that is based on comparisons of cellular fitness. This study used a series of genetic tests in Drosophila to explore the relative contribution of the pleiotropic cytokine tumor necrosis factor α (TNFα) in Myc-mediated cell competition (also known as Myc supercompetition or Myc cell competition). The sole Drosophila TNF, Eiger (Egr), its receptor Grindelwald (Grnd/TNF receptor), and the adaptor proteins Traf4 and Traf6 were found to be required to eliminate wild-type "loser" cells during Myc cell competition. Although typically the interaction between Egr and Grnd leads to cell death by activating the intracellular Jun N-terminal kinase (JNK) stress signaling pathway, these experiments reveal that many components of canonical JNK signaling are dispensable for cell death in Myc cell competition, including the JNKKK Tak1, the JNKK Hemipterous and the JNK Basket. These results suggest that Egr/Grnd signaling participates in Myc cell competition but functions in a role that is largely independent of the JNK signaling pathway.

Wang, X., Cupo, C. M., Ostvar, S., Countryman, A. D., Kasza, K. E. (2024). E-cadherin tunes tissue mechanical behavior before and during morphogenetic tissue flows. Curr Biol, 34(15):3367-3379.e3365 PubMed ID: 39013464
Summary:
Adhesion between epithelial cells enables the remarkable mechanical behavior of epithelial tissues during morphogenesis. However, it remains unclear how cell-cell adhesion influences mechanics in both static and dynamically flowing conflue.,nt epithelial tissues. This study systematically modulated E-cadherin-mediated adhesion in the Drosophila embryo and studied the effects on the mechanical behavior of the germband epithelium before and during dramatic tissue remodeling and flow associated with body axis elongation. Before axis elongation, increasing E-cadherin levels waa found to produces tissue comprising more elongated cells and predicted to be more fluid-like, providing reduced resistance to tissue flow. During axis elongation, the dominant effect of E-cadherin is tuning the speed at which cells proceed through rearrangement events. Before and during axis elongation, E-cadherin levels influence patterns of actomyosin-dependent forces, supporting the notion that E-cadherin tunes tissue mechanics in part through effects on actomyosin. Notably, the effects of ~4-fold changes in E-cadherin levels on overall tissue structure and flow are relatively weak, suggesting that the system is tolerant to changes in absolute E-cadherin levels over this range where an intact tissue is formed. Taken together, these findings reveal dual-and sometimes opposing-roles for E-cadherin-mediated adhesion in controlling tissue structure and dynamics in vivo, which result in unexpected relationships between adhesion and flow in confluent tissues.

Nelson, K. A., Lenhart, K. F., Anllo, L., DiNardo, S. (2024). The Drosophila hematopoietic niche assembles through collective cell migration controlled by neighbor tissues and Slit-Robo signaling. bioRxiv, PubMed ID: 38979182
Summary:
Niches are often found in specific positions in tissues relative to the stem cells they support. Consistency of niche position suggests that placement is important for niche function. However, the complexity of most niches has precluded a thorough understanding of how their proper placement is established. This study investigated the formation of a genetically tractable niche, the Drosophila Posterior Signaling Center (PSC), the assembly of which had not been previously explored. This niche controls hematopoietic progenitors of the lymph gland (LG). PSC cells were previously shown to be specified laterally in the embryo, but ultimately reside dorsally, at the LG posterior. Using live-imaging this study showed that PSC cells migrate as a tight collective and associate with multiple tissues during their trajectory to the LG posterior. Slit emanating from two extrinsic sources, visceral mesoderm and cardioblasts, is required for the PSC to remain a collective, and for its attachment to cardioblasts during migration. Without proper Slit-Robo signaling, PSC cells disperse, form aberrant contacts, and ultimately fail to reach their stereotypical position near progenitors. This work characterizes a novel example of niche formation and identifies an extrinsic signaling relay that controls precise niche positioning.

Matthew, J., Vishwakarma, V., Le, T. P., Agsunod, R. A., Chung, S. (2024). Coordination of cell cycle and morphogenesis during organ formation. Elife, 13 PubMed ID: 38275142
Summary:
Organ formation requires precise regulation of cell cycle and morphogenetic events. Using the Drosophila embryonic salivary gland (SG) as a model, the role of the SP1/KLF transcription factor Huckebein (Hkb) in coordinating cell cycle regulation and morphogenesis was uncovered. The hkb mutant SG exhibits defects in invagination positioning and organ size due to the abnormal death of SG cells. Normal SG development involves distal-to-proximal progression of endoreplication (endocycle), whereas hkb mutant SG cells undergo abnormal cell division, leading to cell death. Hkb represses the expression of key and pro-apoptotic genes in the SG. Knockdown of cyclin E or cyclin-dependent kinase 1, or overexpression of fizzy-related rescues most of the morphogenetic defects observed in the hkb mutant SG. These results indicate that Hkb plays a critical role in controlling endoreplication by regulating the transcription of key cell cycle effectors to ensure proper organ formation.

Athilingam, T., Nelanuthala, A. V. S., Breen, C., Karedla, N., Fritzsche, M., Wohland, T., Saunders, T. E. (2024). Long-range formation of the Bicoid gradient requires multiple dynamic modes that spatially vary across the embryo. Development, 151(3) PubMed ID: 38345326
Summary:
Morphogen gradients provide essential positional information to gene networks through their spatially heterogeneous distribution, yet how they form is still hotly contested, with multiple models proposed for different systems. This study focused on the transcription factor Bicoid (Bcd), a morphogen that forms an exponential gradient across the anterior-posterior (AP) axis of the early Drosophila embryo. Using fluorescence correlation spectroscopy it was found there are spatial differences in Bcd diffusivity along the AP axis, with Bcd diffusing more rapidly in the posterior. Such spatially varying differences in Bcd dynamics are sufficient to explain how Bcd can have a steep exponential gradient in the anterior half of the embryo and yet still have an observable fraction of Bcd near the posterior pole. In the nucleus, we demonstrate that Bcd dynamics are impacted by binding to DNA. Addition of the Bcd homeodomain to eGFP::NLS qualitatively replicates the Bcd concentration profile, suggesting this domain regulates Bcd dynamics. These results reveal how a long-range gradient can form while retaining a steep profile through much of its range.

Tuesday April 22st - Behavior

Easwaran, S., Montell, D. J. (2024). A genome-wide association study implicates the olfactory system in Drosophila melanogaster diapause-associated lifespan extension and fecundity. bioRxiv, PubMed ID: 39005458
Summary:
The effects of environmental stress on animal life are gaining importance with climate change. Diapause is a dormancy program that occurs in response to an adverse environment, followed by resumption of development and reproduction upon the return of favorable conditions. Diapause is a complex trait, so this study leveraged the Drosophila genetic reference panel (DGRP) lines and conducted a Genome-Wide Association Study (GWAS) to characterize the genetic basis of diapause. Post-diapause and non-diapause fecundity was assessed pacross 193 DGRP lines. GWAS revealed 546 genetic variants, encompassing single nucleotide polymorphisms, insertions and deletions associated with post-diapause fecundity. 291 candidate diapause-associated genes were identified, 40 of which had previously been associated with diapause. 89 of the candidates were associated with more than one SNP. Gene network analysis indicated that the diapause-associated genes were primarily linked to neuronal and reproductive system development. Similarly, comparison with results from other fly GWAS revealed the greatest overlap with olfactory-behavior-associated and fecundity-and-lifespan-associated genes. An RNAi screen of the top candidates identified two neuronal genes, Dip-γ and Scribbler, to be required during recovery for post-diapause fecundity. The genetic analysis was complemented with a test of which neurons are required for successful diapause. Athough amputation of the antenna had little to no effect on non-diapause lifespan, it reduced diapause lifespan and postdiapause fecundity. It was further shown that olfactory receptor neurons and temperature-sensing neurons are required for successful recovery from diapause. These results provide insights into the molecular, cellular, and genetic basis of adult reproductive diapause in Drosophila .

Haustein, M., Blanke, A., Bockemuhl, T., Buschges, A. (2024). A leg model based on anatomical landmarks to study 3D joint kinematics of walking in Drosophila melanogaster. Frontiers in bioengineering and biotechnology, 12:1357598 PubMed ID: 38988867
Summary:
fWalking is the most common form of how animals move on land. The model organism Drosophila melanogaster has become increasingly popular for studying how the nervous system controls behavior in general and walking in particular. Despite recent advances in tracking and modeling leg movements of walking Drosophila in 3D, there are still gaps in knowledge about the biomechanics of leg joints due to the tiny size of fruit flies. For instance, the natural alignment of joint rotational axes was largely neglected in previous kinematic analyses. This study therefore presents a detailed kinematic leg model in which not only the segment lengths but also the main rotational axes of the joints were derived from anatomical landmarks, namely, the joint condyles. The model with natural oblique joint axes is able to adapt to the 3D leg postures of straight and forward walking fruit flies with high accuracy. When the model was compared to an orthogonalized version, it was observed that the model showed a smaller error as well as differences in the used range of motion (ROM), highlighting the advantages of modeling natural rotational axes alignment for the study of joint kinematics. It was further found that the kinematic profiles of front, middle, and hind legs differed in the number of required degrees of freedom as well as their contributions to stepping, time courses of joint angles, and ROM. These findings provide deeper insights into the joint kinematics of walking in Drosophila, and, additionally, will help to develop dynamical, musculoskeletal, and neuromechanical simulations.

He, Y., Ding, Y., Gong, C., Zhou, J., Gong, Z. (2024). The tail segments are required by the performance but not the accomplishment of various modes of Drosophila larval locomotion. Behav Brain Res, 471:115074 PubMed ID: 38825023
Summary:
The tail plays important roles in locomotion control in many animals. But in animals with multiple body segments, the roles of the hind body segments and corresponding innervating neurons in locomotion control are not clear. Using the Drosophila larva as the model animal, this study investigated the roles of the posterior terminal segments in various modes of locomotion and found that they participate in all of them. In forward crawling, paralysis of the larval tail by blocking the Abdb-Gal4 labeled neurons in the posterior segments of VNC led to a slower locomotion speed but did not prevent the initiation of forward peristalsis. In backward crawling, larvae with the Abdb-Gal4 neurons inhibited were unable to generate effective displacement although waves of backward peristalsis could be initiated and persist. In head swing where the movement of the tail is not obvious, disabling the larval tail by blocking Abdb-Gal4 neurons led to increased bending amplitude upon touching the head. In the case of larval lateral rolling, larval tail paralysis by inhibition of Abdb-Gal4 neurons did not prevent the accomplishment of rolling, but resulted in slower rolling speed. This work reveals that the contribution of Drosophila larval posterior VNC segments and corresponding body segments in the tail to locomotion is comprehensive but could be compensated at least partially by other body segments. It is suggested that the decentralization in locomotion control with respect to animal body parts helps to maintain the robustness of locomotion in multi-segment animals.

Canic, T., Lopez, J., Ortiz-Vega, N., Zhai, R. G., Syed, S. (2024). High-resolution, high-throughput analysis of Drosophila geotactic behavior. bioRxiv, PubMed ID: 38895419
Summary:
Drosophila innate response to gravity, geotaxis, has been previously used to assess the impact of aging and disease on motor performance. Despite its rich history, fly geotaxis continues to be largely measured manually and assessed through simplistic metrics. The manual nature of this assay introduces substantial experimental variability while simplistic metrics provide limited analytic insights into the behavior. To address these shortcomings, this study has constructed a fully automated, programable apparatus, and developed a multi-object tracking software capable of following sub-second movements of individual flies, thus allowing reproducible, detailed, and quantitative analysis of geotactic behavior. The apparatus triggers and monitors geotaxis of 10 fly cohorts simultaneously, with each cohort consisting of up to 7 flies. The tracking program isolates cohorts and records individual fly coordinate outputs allowing for simultaneous multi-group, multi-fly tracks per experiment, greatly improving throughput and resolution. The algorithm tracks individual flies during the entire run with ~97% accuracy, yielding detailed climbing curve, speed, and movement direction with 1/30 second resolution. This tracking also allows the construction of multi-variable metrics and the detection of transitory movement phenotypes, such as slips and falls, which have thus far been neglected in geotaxis studies due to limited spatio-temporal resolution. Through a combination of automation and robust tracking, the platform is therefore poised to advance Drosophila geotaxis assay into a comprehensive assessment of locomotor behavior.

Pajusalu, M., Seager, S., Huang, J., Petkowski, J. J. (2024). A qualitative assessment of limits of active flight in low density atmospheres. Sci Rep, 14(1):13823 PubMed ID: 38879676
Summary:
Exoplanet atmospheres are expected to vary significantly in thickness and chemical composition, leading to a continuum of differences in surface pressure and atmospheric density. This variability is exemplified within our Solar System, where the four rocky planets exhibit surface pressures ranging from 1 nPa on Mercury to 9.2 MPa on Venus. The direct effects and potential challenges of atmospheric pressure and density on life have rarely been discussed. For instance, atmospheric density directly affects the possibility of active flight in organisms, a critical factor since without it, dispersing across extensive and inhospitable terrains becomes a major limitation for the expansion of complex life. This paper proposes the existence of a critical atmospheric density threshold below which active flight is unfeasible, significantly impacting biosphere development. To qualitatively assess this threshold and differentiate it from energy availability constraints, the limits of active flight on Earth, using the common fruit fly, Drosophila melanogaster, as a model organism.Drosophila melanogaster was subjected to various atmospheric density scenarios, and rprevious data on flight limitations were reviewed. The observations show that flies in an N(2)-enriched environment recover active flying abilities more efficiently than those in a helium-enriched environment, highlighting behavioral differences attributable to atmospheric density vs. oxygen deprivation.

Rauscher, M. J., Fox, J. L. (2024). Asynchronous haltere input drives specific wing and head movements in Drosophila. Proceedings Biological sciences, 291(2024):20240311 PubMed ID: 38864337
Summary:
Halteres are multifunctional mechanosensory organs unique to the true flies (Diptera). A set of reduced hindwings, the halteres beat at the same frequency as the lift-generating forewings and sense inertial forces via mechanosensory campaniform sensilla. Though haltere ablation makes stable flight impossible, the specific role of wing-synchronous input has not been established. Using small iron filings attached to the halteres of tethered flies and an alternating electromagnetic field, the wings and halteres of flying Drosophila were experimentally decoupled, and the resulting changes in wingbeat amplitude and head orientation were observed. Asynchronous haltere input results in fast amplitude changes in the wing (hitches), but does not appreciably move the head. In multi-modal experiments, wing and gaze optomotor responses were disrupted differently by asynchronous input. These effects of wing-asynchronous haltere input suggest that specific sensory information is necessary for maintaining wing amplitude stability and adaptive gaze control.

Monday April 21st - Adult Physiology and Metabolism

Brand, C. L., Oliver, G. T., Farkas, I. Z., Buszczak, M., Levine, M. T. (2024). Recurrent Duplication and Diversification of a Vital DNA Repair Gene Family Across Drosophila. Mol Biol Evol, 41(6) PubMed ID: 38865490
Summary:
Maintaining genome integrity is vital for organismal survival and reproduction. Essential, broadly conserved DNA repair pathways actively preserve genome integrity. However, many DNA repair proteins evolve adaptively. Ecological forces like UV exposure are classically cited drivers of DNA repair evolution. Intrinsic forces like repetitive DNA, which also imperil genome integrity, have received less attention. We recently reported that a Drosophila melanogaster-specific DNA satellite array triggered species-specific, adaptive evolution of a DNA repair protein called Spartan>/?/MH. The Spartan family of proteases cleave hazardous, covalent crosslinks that form between DNA and proteins ("DNA-protein crosslink repair"). Appreciating that DNA satellites are both ubiquitous and universally fast-evolving, we hypothesized that satellite DNA turnover spurs adaptive evolution of DNA-protein crosslink repair beyond a single gene and beyond the D. melanogaster lineage. This hypothesis predicts pervasive Spartan gene family diversification across Drosophila species. To study the evolutionary history of the Drosophila Spartan gene family, we conducted population genetic, molecular evolution, phylogenomic, and tissue-specific expression analyses. We uncovered widespread signals of positive selection across multiple Spartan family genes and across multiple evolutionary timescales. We also detected recurrent Spartan family gene duplication, divergence, and gene loss. Finally, we found that ovary-enriched parent genes consistently birthed functionally diverged, testis-enriched daughter genes. To account for Spartan family diversification, we introduce a novel mechanistic model of antagonistic coevolution that links DNA satellite evolution and adaptive regulation of Spartan protease activity. This framework promises to accelerate our understanding of how DNA repeats drive recurrent evolutionary innovation to preserve genome integrity.

Kotov, A. A., Adashev, V. E., Kombarov, I. A., Bazylev, S. S., Shatskikh, A. S., Olenina, L. V. (2024). Molecular Insights into Female Hybrid Sterility in Interspecific Crosses between Drosophila melanogaster and Drosophila simulans. Int J Mol Sci, 25(11) PubMed ID: 38891872
Summary:
Species of the genus Drosophila have served as favorite models in speciation studies; however, genetic factors of interspecific reproductive incompatibility are under-investigated. This study performed an analysis of hybrid female sterility by crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis and molecular, cellular, and genetic approaches, differential gene expression, transposable element (TE) activity, piRNA biogenesis, and functional defects of oogenesis in hybrids were studied. Premature germline stem cell loss was the most prominent defect of oogenesis in hybrid ovaries. Because of the differential expression of genes encoding piRNA pathway components, rhino and deadlock, the functional RDC(mel) complex in hybrid ovaries was not assembled. However, the activity of the RDC(sim) complex was maintained in hybrids independent of the genomic origin of piRNA clusters. Despite the identification of a cohort of overexpressed TEs in hybrid ovaries, no evidence was found that their activity can be considered the main cause of hybrid sterility. A complicated pattern of Vasa protein expression was observed in the hybrid germline, including partial AT-chX piRNA targeting of the vasa^sim allele and a significant zygotic delay in vasa^mel/sup> expression. The conclusion was drawned that the hybrid sterility phenotype was caused by intricate multi-locus differences between the species.

Wiseglass, G., Rubinstein, R. (2024). Following the Evolutionary Paths of Dscam1 Proteins toward Highly Specific Homophilic Interactions. Mol Biol Evol, 41(7) PubMed ID: 38989909
Summary:
Many adhesion proteins, evolutionarily related through gene duplication, exhibit distinct and precise interaction preferences and affinities crucial for cell patterning. Yet, the evolutionary paths by which these proteins acquire new specificities and prevent cross-interactions within their family members remain unknown. To bridge this gap, this study focuses on Drosophila Down syndrome cell adhesion molecule-1 (Dscam1) proteins, which are cell adhesion proteins that have undergone extensive gene duplication. Dscam1 evolved under strong selective pressure to achieve strict homophilic recognition, essential for neuronal self-avoidance and patterning. Through a combination of phylogenetic analyses, ancestral sequence reconstruction, and cell aggregation assays, we studied the evolutionary trajectory of Dscam1 exon 4 across various insect lineages. We demonstrated that recent Dscam1 duplications in the mosquito lineage bind with strict homophilic specificities without any cross-interactions. We found that ancestral and intermediate Dscam1 isoforms maintained their homophilic binding capabilities, with some intermediate isoforms also engaging in promiscuous interactions with other paralogs. Our results highlight the robust selective pressure for homophilic specificity integral to the Dscam1 function within the process of neuronal self-avoidance. Importantly, our study suggests that the path to achieving such selective specificity does not introduce disruptive mutations that prevent self-binding but includes evolutionary intermediates that demonstrate promiscuous heterophilic interactions. Overall, these results offer insights into evolutionary strategies that underlie adhesion protein interaction specificities.

Joyce, M., Falconio, F. A., Blackhurst, L., Prieto-Godino, L., French, A. S., Gilestro, G. F. (2024). Divergent evolution of sleep in Drosophila species. Nat Commun, 15(1):5091 PubMed ID: 38876988
Summary:
Living organisms synchronize their biological activities with the earth's rotation through the circadian clock, a molecular mechanism that regulates biology and behavior daily. This synchronization factually maximizes positive activities (e.g., social interactions, feeding) during safe periods, and minimizes exposure to dangers (e.g., predation, darkness) typically at night. Beyond basic circadian regulation, some behaviors like sleep have an additional layer of homeostatic control, ensuring those essential activities are fulfilled. While sleep is predominantly governed by the circadian clock, a secondary homeostatic regulator, though not well-understood, ensures adherence to necessary sleep amounts and hints at a fundamental biological function of sleep beyond simple energy conservation and safety. This study explored sleep regulation across seven Drosophila species with diverse ecological niches, revealing that while circadian-driven sleep aspects are consistent, homeostatic regulation varies significantly. The findings suggest that in Drosophilids, sleep evolved primarily for circadian purposes. The more complex, homeostatically regulated functions of sleep appear to have evolved independently in a species-specific manner, and are not universally conserved. This laboratory model may reproduce and recapitulate primordial sleep evolution.

Roy, P. R., Castillo, D. M. (2024). The neurodevelopmental genes alan shepard and Neuroglian contribute to female mate preference in African Drosophila melanogaster. J Evol Biol, 37(8):877-890 PubMed ID: 38900077
Summary:
Mate choice is a key trait that determines fitness for most sexually reproducing organisms, with females often being the choosy sex. Female preference often results in strong selection on male traits that can drive rapid divergence of traits and preferences between lineages, leading to reproductive isolation. Despite this fundamental property of female mate choice, very few loci have been identified that contribute to mate choice and reproductive isolation. This study used a combination of population genetics, quantitative complementation tests, and behavioural assays to demonstrate that alan shepard and Neuroglian contribute to female mate choice, and could contribute to partial reproductive isolation between populations of Drosophila melanogaster. This study is among the first to identify genes that contribute to female mate preference in this historically important system, where female preference is an active premating barrier to reproduction. The identification of loci that are primarily known for their roles in neurodevelopment provides intriguing questions of how female mate preference evolves in populations via changes in sensory system and higher learning brain centres.

Ridges, J. T., Bladen, J., King, T. D., Brown, N. C., Large, C. R. L., Cooper, J. C., Jones, A. J., Loppin, B., Dubruille, R., Phadnis, N. (2024). Overdrive is essential for targeted sperm elimination by Segregation Distorter. JbioRxiv, PubMed ID: 38895353
Summary:
Intra-genomic conflict driven by selfish chromosomes is a powerful force that shapes the evolution of genomes and species. In the male germline, many selfish chromosomes bias transmission in their own favor by eliminating spermatids bearing the competing homologous chromosomes. However, the mechanisms of targeted gamete elimination remain mysterious. This study shows that Overdrive (Ovd), a gene required for both Responder spermatid elimination after the histone-to-protamine transition in the classical Segregation Distorter system. It is proposed that Ovd functions as a general spermatid quality checkpoint that is hijacked by independent selfish chromosomes to eliminate competing gametes.

Friday April 18th - Adult Physiology and Metabolism

Niosi, A., Vo, N. H., Sundaramurthy, P., ..., Jensen, M. H., Mulligan, K. (2024). Kismet/CHD7/CHD8 affects gut microbiota, mechanics, and the gut-brain axis in Drosophila melanogaster. Biophys J, PubMed ID: 38902926
Summary:
The gut microbiome affects brain and neuronal development and may contribute to the pathophysiology of neurodevelopmental disorders. However, it is unclear how risk genes associated with such disorders affect gut physiology in a manner that could impact microbial colonization and how the mechanical properties of the gut tissue might play a role in gut-brain bidirectional communication. To address this, Drosophila melanogaster was used with a null mutation in the gene kismet, an ortholog of chromodomain helicase DNA-binding protein (CHD) family members CHD7 and CHD8. In humans, these are risk genes for neurodevelopmental disorders with co-occurring gastrointestinal symptoms. kismet mutant flies have a significant increase in gastrointestinal transit time, indicating the functional homology of kismet with CHD7/CHD8 in vertebrates. Rheological characterization of dissected gut tissue revealed significant changes in the mechanics of kismet mutant gut elasticity, strain stiffening behavior, and tensile strength. Using 16S rRNA metagenomic sequencing, it was also found that kismet mutants have reduced diversity and abundance of gut microbiota at every taxonomic level. To investigate the connection between the gut microbiome and behavior, gut microbiota were depleted in kismet mutant and control flies and quantified the flies' courtship behavior. Depletion of gut microbiota rescued courtship defects of kismet mutant flies, indicating a connection between gut microbiota and behavior. In striking contrast, depletion of the gut microbiome in the control strain reduced courtship activity, demonstrating that antibiotic treatment can have differential impacts on behavior and may depend on the status of microbial dysbiosis in the gut prior to depletion.

Ye, Y. Y., Liu, Z. H., Wang, H. L. (2024). Fat body-derived juvenile hormone acid methyltransferase functions to maintain iron homeostasis in Drosophila melanogaster. Faseb j, 38(14):e23805 PubMed ID: 39003630
Summary:
Iron homeostasis is of critical importance to living organisms. Drosophila melanogaster has emerged as an excellent model to study iron homeostasis, while the regulatory mechanism of iron metabolism remains poorly understood. This study accidently found that knockdown of juvenile hormone (JH) acid methyltransferase (Jhamt) specifically in the fat body, a key rate-limiting enzyme for JH synthesis, led to iron accumulation locally, resulting in serious loss and dysfunction of fat body. Jhamt knockdown-induced phenotypes were mitigated by iron deprivation, antioxidant and Ferrostatin-1, a well-known inhibitor of ferroptosis, suggesting ferroptosis was involved in Jhamt knockdown-induced defects in the fat body. Further study demonstrated that upregulation of Tsf1 and Malvolio (Mvl, homolog of mammalian DMT1), two iron importers, accounted for Jhamt knockdown-induced iron accumulation and dysfunction of the fat body. Mechanistically, Kr-h1, a key transcription factor of JH, acts downstream of Jhamt inhibiting Tsf1 and Mvl transcriptionally. In summary, the findings indicated that fat body-derived Jhamt is required for the development of Drosophila by maintaining iron homeostasis in the fat body, providing unique insight into the regulatory mechanisms of iron metabolism in Drosophila.

Gera, J., Kumar, D., Chauhan, G., Choudhary, A., Rani, L., Mandal, L., Mandal, S. (2024). High sugar diet-induced fatty acid oxidation potentiates cytokine-dependent cardiac ECM remodeling. J Cell Biol, 223(9) PubMed ID: 38916917
Summary:
Context-dependent physiological remodeling of the extracellular matrix (ECM) is essential for development and organ homeostasis. On the other hand, consumption of high-caloric diet leverages ECM remodeling to create pathological conditions that impede the functionality of different organs, including the heart. However, the mechanistic basis of high caloric diet-induced ECM remodeling has yet to be elucidated. Employing in vivo molecular genetic analyses in Drosophila, this study demonstrated that high dietary sugar triggers ROS-independent activation of JNK signaling to promote fatty acid oxidation (FAO) in the pericardial cells (nephrocytes). An elevated level of FAO, in turn, induces histone acetylation-dependent transcriptional upregulation of the cytokine Unpaired 3 (Upd3). Release of pericardial Upd3 augments fat body-specific expression of the cardiac ECM protein Pericardin, leading to progressive cardiac fibrosis. Importantly, this pathway is quite distinct from the ROS-Ask1-JNK/p38 axis that regulates Upd3 expression under normal physiological conditions. These results unravel an unknown physiological role of FAO in cytokine-dependent ECM remodeling, bearing implications in diabetic fibrosis.

Miyamoto, T., Hedjazi, S., Miyamoto, C., Amrein, H. (2024). Drosophila neuronal Glucose-6-Phosphatase is a modulator of neuropeptide release that regulates muscle glycogen stores via FMRFamide signaling. Proc Natl Acad Sci U S A, 121(30):e2319958121 PubMed ID: 39008673
Summary:
Neuropeptides (NPs) and their cognate receptors are critical effectors of diverse physiological processes and behaviors. A noncanonical function of the Drosophila Glucose-6-Phosphatase (G6P) gene has ben recently reported in a subset of neurosecretory cells in the central nervous system that governs systemic glucose homeostasis in food-deprived flies. This study shows that G6P-expressing neurons define six groups of NP-secreting cells, four in the brain and two in the thoracic ganglion. Using the glucose homeostasis phenotype as a screening tool, it was found that neurons located in the thoracic ganglion expressing FMRFamide NPs (FMRFa(G6P) neurons) are necessary and sufficient to maintain systemic glucose homeostasis in starved flies. It was further shown that G6P is essential in FMRFa(G6P) neurons for attaining a prominent Golgi apparatus and secreting NPs efficiently. Finally, G6P-dependent FMRFa signaling was established as essential for the build-up of glycogen stores in the jump muscle which expresses the receptor for FMRFamides. A general model is proposed in which the main role of G6P is to counteract glycolysis in peptidergic neurons for the purpose of optimizing the intracellular environment best suited for the expansion of the Golgi apparatus, boosting release of NPs and enhancing signaling to respective target tissues expressing cognate receptors.

Pandey, P., Shrestha, B., Lee, Y. (2024). Avoiding alkaline taste through ionotropic receptors. iScience, 27(6):110087 PubMed ID: 38947501
Summary:
Taste organsZ contain distinct gustatory receptors that help organisms differentiate between nourishing and potentially harmful foods. The detection of high pH levels plays a crucial role in food selection, but the specific gustatory receptors responsible for perceiving elevated pH in foods have remained unknown. By using Drosophila melanogaster as a model organism, this study has uncovered the involvement of ionotropic receptors (IRs) in avoiding high-pH foods. This study involved a combination of behavioral tests and electrophysiological analyses, which led to the identification of six Irs from bitter-sensing gustatory receptor neurons essential for rejecting food items with elevated pH levels. Using the same methodology, this study reevaluated the significance and OtopLa. The findings highlight that Alka, in conjunction with IRs, is crucial for detecting alkaline substances, whereas OtopLa does not contribute to this process. Overall, this study offers valuable insights into the intricate mechanisms governing taste perception in organisms.

Chu, S. Y., Lai, Y. W., Hsu, T. C., Lu, T. M., Yu, H. H. (2024). Isoforms of terminal selector Mamo control axon guidance during adult Drosophila memory center construction via Semaphorin-1a. Dev Biol, 515:1-6 PubMed ID: 38906235
Summary:
In animals undergoing metamorphosis, the appearance of the nervous system is coincidently transformed by the morphogenesis of neurons. Such morphogenic alterations are exemplified in three types of intrinsic neurons in the Drosophila memory center. In contrast to the well-characterized remodeling of γ neurons, the morphogenesis of α/β and α'/β' neurons has not been adequately explored. This study showed that mamo a BTB-zinc finger transcription factor that acts as a terminal selector for α'/β' neurons, controls the formation of the correct axonal pattern of α'/β' neurons. Intriguingly, specific Mamo isoforms are preferentially expressed in α'/β' neurons to regulate the expression of axon guidance molecule Semaphorin-1a. This action directs proper axon guidance in α'/β' neurons, which is also crucial for wiring of α'/β' neurons with downstream neurons. Taken together, these results provide molecular insights into how neurons establish correct axonal patterns in circuitry assembly during adult memory center construction.

Wednesday April 16th - Synapse and Vesicles

Ferng, D., Sun, W., Shieh, B. H. (2024). Differential activation of rhodopsin triggers distinct endocytic trafficking and recycling in vivo via differential phosphorylation. PLoS One, 19(6):e0303882 PubMed ID: 38848405
Summary:
Activated GPCRs are phosphorylated and internalized mostly via clathrin-mediated endocytosis (CME), and are then sorted for recycling or degradation. This study investigated how differential activation of the same GPCR affects its endocytic trafficking in vivo using rhodopsin as a model in pupal photoreceptors of flies expressing mCherry-tagged rhodopsin 1 (Rh1-mC) or GFP-tagged arrestin 1 (Arr1-GFP). Upon blue light stimulation, activated Rh1 recruited Arr1-GFP to the rhabdomere, which became co-internalized and accumulated in cytoplasmic vesicles of photoreceptors. This internalization was eliminated in shi^ts1 mutants affecting dynamin. Moreover, it was blocked by either rdgA or rdgB mutations affecting the PIP2 biosynthesis. Together, the blue light-initiated internalization of Rh1 and Arr1 belongs to CME. Green light stimulation also triggered the internalization and accumulation of activated Rh1-mC in the cytoplasm but with faster kinetics. Importantly, Arr1-GFP was also recruited to the rhabdomere but not co-internalized with Rh1-mC. This endocytosis was not affected in shi^ts1 nor rdgA mutants, indicating it is not CME. The fate of internalized Rh1-mC following CME was examined and it remained in cytoplasmic vesicles following 30 min of dark adaptation. In contrast, in the non-CME Rh1-mC appeared readily recycled back to the rhabdomere within five min of dark treatment. This faster recycling may be regulated by rhodopsin phosphatase, RdgC. Together, two distinct endocytic and recycling mechanisms of Rh1 were demonstrated via two light stimulations. It appears that each stimulation triggers a distinct conformation leading to different phosphorylation patterns of Rh1 capable of recruiting Arr1 to rhabdomeres. However, a more stable interaction leads to the co-internalization of Arr1 that orchestrates CME. A stronger Arr1 association appears to impede the recycling of the phosphorylated Rh1 by preventing the recruitment of RdgC. It is concluded that conformations of activated rhodopsin determine the downstream outputs upon phosphorylation that confers differential protein-protein interactions.

Madan, A., Kelly, K. P., Bahk, P., Sullivan, C. E., Poling, M. E., Brent, A. E., Alassaf, M., Dubrulle, J., Rajan, A. (2024). Atg8/LC3 controls systemic nutrient surplus signaling in flies and humans. Curr Biol, 34(15):3327-3341PubMed ID: 38955177
Summary:
Organisms experience constant nutritional flux. Mechanisms at the interface of opposing nutritional states-scarcity and surplus-enable organismal energy homeostasis. Contingent on nutritional stores, adipocytes secrete adipokines, such as the fat hormone leptin, to signal nutrient status to the central brain. Increased leptin secretion underlies metabolic dysregulation during common obesity, but the molecular mechanisms regulating leptin secretion from human adipocytes are poorly understood. Here, we report that Atg8/LC3 family proteins, best known for their role in autophagy during nutrient scarcity, play an evolutionarily conserved role during nutrient surplus by promoting adipokine secretion. We show that in a well-fed state, Atg8/LC3 promotes the secretion of the Drosophila functional leptin ortholog unpaired 2 (Upd2) and leptin from human adipocytes. Proteomic analyses reveal that LC3 directs leptin to a secretory pathway in human cells. We identified LC3-dependent extracellular vesicle (EV) loading and secretion (LDELS) as a required step for leptin release, highlighting a unique secretory route adopted by leptin in human adipocytes. In Drosophila, mutations to Upd2's Atg8 interaction motif (AIM) result in constitutive adipokine retention. Atg8-mediated Upd2 retention alters lipid storage and hunger response and rewires the bulk organismal transcriptome in a manner conducive to starvation survival. Thus, Atg8/LC3's bidirectional role in nutrient sensing-conveying nutrient surplus and responding to nutrient deprivation-enables organisms to manage nutrient flux effectively. We posit that decoding how bidirectional molecular switches-such as Atg8/LC3-operate at the nexus of nutritional scarcity and surplus will inform therapeutic strategies to tackle chronic metabolic disorders.

Christophers, B., Leahy, S. N., Soffar, D. B., von Saucken, V. E., Broadie, K., Baylies, M. K. (2024). Muscle cofilin alters neuromuscular junction postsynaptic development to strengthen functional neurotransmission. Development, 151(13) PubMed ID: 38869008
Summary:
Cofilin, an actin-severing protein, plays key roles in muscle sarcomere addition and maintenance. Previous work found that Drosophila cofilin (DmCFL) knockdown in muscle causes progressive deterioration of muscle structure and function and produces features seen in nemaline myopathy caused by cofilin mutations. It was hypothesized that disruption of actin cytoskeleton dynamics by DmCFL knockdown would impact other aspects of muscle development, and, thus, an RNA-sequencing analysis was conducted that unexpectedly revealed upregulated expression of numerous neuromuscular junction (NMJ) genes. DmCFL is enriched in the muscle postsynaptic compartment, and DmCFL muscle knockdown causes F-actin disorganization in this subcellular domain prior to the sarcomere defects observed later in development. Despite NMJ gene expression changes, no significant changes were found in gross presynaptic Bruchpilot active zones or total postsynaptic glutamate receptor levels. However, DmCFL knockdown resulted in mislocalization of GluRIIA class glutamate receptors in more deteriorated muscles and strongly impaired NMJ transmission strength. These findings expand understanding of the roles of cofilin in muscle to include NMJ structural development and suggest that NMJ defects may contribute to the pathophysiology of nemaline myopathy.

Malis, Y., Armoza-Eilat, S., Nevo-Yassaf, I., Dukhovny, A., Sklan, E. H., Hirschberg, K. (2024). Rab1b facilitates lipid droplet growth by ER-to-lipid droplet targeting of DGAT2. Sci Adv, 10(22):eade7753 PubMed ID: 38809969
Summary:
Lipid droplets (LDs) comprise a triglyceride core surrounded by a lipid monolayer enriched with proteins, many of which function in LD homeostasis. How proteins are targeted to the growing LD is still unclear. Rab1b (Drosophila homolog: Rab1), a GTPase regulating secretory transport, was recently associated with targeting proteins to LDs in a Drosophila RNAi screen. LD formation was prevented in human hepatoma cells overexpressing dominant-negative Rab1b. It was thus hypothesized that Rab1b recruits lipid-synthesizing enzymes, facilitating LD growth. Here, FRET between diacylglycerol acyltransferase 2 (DGAT2) and Rab1b and activity mutants of the latter demonstrated that Rab1b promotes DGAT2 ER to the LD surface redistribution. Last, alterations in LD metabolism and DGAT2 redistribution, consistent with Rab1b activity, were caused by mutations in the Rab1b-GTPase activating protein TBC1D20 in Warburg Micro syndrome (WARBM) model mice fibroblasts. These data contribute to understanding of the mechanism of Rab1b in LD homeostasis and WARBM, a devastating autosomal-recessive disorder caused by mutations in TBC1D20.

Han, T. H., Vicidomini, R., Ramos, C. I., Mayer, M., Serpe, M. (2024). Neto proteins differentially modulate the gating properties of Drosophila NMJ glutamate receptors. bioRxiv, PubMed ID: 38903091
Summary:
The formation of functional synapses requires co-assembly of ion channels with their accessory proteins which controls where, when, and how neurotransmitter receptors function. The auxiliary protein Neto modulates the function of kainate-type glutamate receptors in vertebrates as well as at the Drosophila neuromuscular junction (NMJ), a glutamatergic synapse widely used for genetic studies on synapse development. Previous work showed that Neto is essential for the synaptic recruitment and function of glutamate receptors. Using outside-out patch-clamp recordings and fast ligand application, this study examined the biophysical properties of recombinant Drosophila NMJ receptors expressed in HEK293T cells and compare them with native receptor complexes of genetically controlled composition. The two Neto isoforms, Neto-α and Neto-β, differentially modulate the gating properties of NMJ receptors. Surprisingly, it was found that deactivation is extremely fast and that the decay of synaptic currents resembles the rate of iGluR desensitization. The functional analyses of recombinant iGluRs that is reported in this study should greatly facilitate the interpretation of compound in vivo phenotypes of mutant animals.

Jay, T. R., Kang, Y., Ouellet-Massicotte, V., Micael, M. K. B., Kacouros-Perkins, V. L., Chen, J., Sheehan, A., Freeman, M. R. (2024). Developmental and age-related synapse elimination is mediated by glial Croquemort. bioRxiv, PubMed ID: 39026803
Summary:
Neurons and glia work together to dynamically regulate neural circuit assembly and maintenance. This study shows Drosophila exhibit large-scale synapse formation and elimination as part of normal CNS circuit maturation, and that glia use conserved molecules to regulate these processes. Using a high throughput ELISA-based in vivo screening assay, new glial genes were identified that regulate synapse numbers in Drosophila in vivo, including the scavenger receptor ortholog Croquemort (Crq). Crq acts as an essential regulator of glial-dependent synapse elimination during development, with glial Crq loss leading to excess CNS synapses and progressive seizure susceptibility in adults. Loss of Crq in glia also prevents age-related synaptic loss in the adult brain. This work provides new insights into the cellular and molecular mechanisms that underlie synapse development and maintenance across the lifespan, and identifies glial Crq as a key regulator of these processes.

Tuesday April 15th - Signaling

Matakatsu, H., Fehon, R. G. (2024). Dachsous and Fat coordinately repress the Dachs-Dlish-Approximated complex to control growth. bioRxiv, PubMed ID: 38948705
Summary:
Two protocadherins, Dachsous (Ds) and Fat (Ft), regulate organ growth in Drosophila via the Hippo pathway. Ds and Ft bind heterotypically to regulate the abundance and subcellular localization of a 'core complex' consisting of Dachs, Dlish and Approximated. This complex localizes to the junctional cortex where it promotes growth by repressing the pathway kinase Warts. Ds is believed to promote growth by recruiting and stabilizing the core complex at the junctional cortex, while Ft represses growth by promoting degradation of core complex components. This study examine the functions of intracellular domains of Ds and Ft and their relationship to the core complex. While Ds promotes accumulation of the core complex proteins in cortical puncta, it is not required for core complex assembly. Indeed, the core complex assembles maximally in the absence of both Ds and Ft. Furthermore, while Ds promotes growth in the presence of Ft, it represses growth in the absence of Ft by removing the core complex from the junctional cortex. Ft similarly recruits core complex components, however it normally promotes their degradation. These findings reveal that Ds and Ft constrain tissue growth by repressing the default 'on' state of the core complex.

Goins, L. M., Girard, J. R., Mondal, B. C., Buran, S., Su, C. C., Tang, R., Biswas, T., Kissi, J. A., Banerjee, U. (2024). Wnt signaling couples G2 phase control with differentiation during hematopoiesis in Drosophila. Dev Cell, PubMed ID: 38866012
Summary:
During homeostasis, a critical balance is maintained between myeloid-like progenitors and their differentiated progeny, which function to mitigate stress and innate immune challenges. The molecular mechanisms that help achieve this balance are not fully understood. Using genetic dissection in Drosophila, this study showed that a /EGFR-signaling network simultaneously controls progenitor growth, proliferation, and differentiation. Unlike G1-quiescence of stem cells, hematopoietic progenitors are blocked in G2 phase by a β-catenin-independent (Wnt/STOP) Wnt6 pathway that restricts nuclear entry and promotes cell growth. Canonical β-catenin-dependent Wnt6 signaling is spatially confined to mature progenitors through localized activation of the tyrosine kinases EGFR and Abelson kinase (Abl), which promote nuclear entry of β-catenin and facilitate exit from G2. This strategy combines transcription-dependent and -independent forms of both Wnt6 and EGFR pathways to create a direct link between cell-cycle control and differentiation. This unique combinatorial strategy employing conserved components may underlie homeostatic balance and stress response in mammalian hematopoiesis.

Wu, J., Bala Tannan, N., Vuong, L. T., Koca, Y., Collu, G. M., Mlodzik, M. (2024). Par3/bazooka binds NICD and promotes notch signaling during Drosophila development. Dev Biol, 514:37-49 PubMed ID: 38885804
Summary:
The conserved bazooka (baz/par3) gene acts as a key regulator of asymmetrical cell divisions across the animal kingdom. Associated Par3/Baz-Par6-aPKC protein complexes are also well known for their role in the establishment of apical/basal cell polarity in epithelial cells. Here we define a novel, positive function of Baz/Par3 in the Notch pathway. Using Drosophila wing and eye development, we demonstrate that Baz is required for Notch signaling activity and optimal transcriptional activation of Notch target genes. Baz appears to act independently of aPKC in these contexts, as knockdown of aPKC does not cause Notch loss-of-function phenotypes. Using transgenic Notch constructs, these data positions Baz activity downstream of activating Notch cleavage steps and upstream of Su(H)/CSL transcription factor complex activity on Notch target genes. A biochemical interaction was demonstrated between NICD and Baz, suggesting that Baz is required for NICD activity before NICD binds to Su(H). Taken together, these data define a novel role of the polarity protein Baz/Par3, as a positive and direct regulator of Notch signaling through its interaction with NICD.

Vuong, L. T., Mlodzik, M. (2024). Wg/Wnt-signaling-induced nuclear translocation of β-catenin is attenuated by a β-catenin peptide through its interference with the IFT-A complex. Cell Rep, 43(6):114362 PubMed ID: 38870008
Summary:
Wnt/Wingless (Wg) signaling is critical in development and disease, including cancer. Canonical Wnt signaling is mediated by β-catenin/Armadillo (Arm in Drosophila) transducing signals to the nucleus, with IFT-A/Kinesin 2 complexes promoting nuclear translocation of β-catenin/Arm. This study demonstrates that a conserved small N-terminal Arm(34)(-)(87)/β-catenin peptide binds to IFT140, acting as a dominant interference tool to attenuate Wg/Wnt signaling in vivo. Arm(34)(-)(87) expression antagonizes endogenous Wnt/Wg signaling, resulting in the reduction of its target expression. Arm(34)(-)(87) inhibits Wg/Wnt signaling by interfering with nuclear translocation of endogenous Arm/β-catenin, and this can be modulated by levels of wild-type β-catenin or IFT140, with the Arm(34)(-)(87) effect being enhanced or suppressed. Importantly, this mechanism is conserved in mammals with the equivalent β-catenin(24)(-)(79) peptide blocking nuclear translocation and pathway activation, including in cancer cells. Our work indicates that Wnt signaling can be regulated by a defined N-terminal β-catenin peptide and thus might serve as an entry point for therapeutic applications to attenuate Wnt/β-catenin signaling.

Kamalesh, K., Segal, D., Avinoam, O., Schejter, E. D., Shilo, B. Z. (2024). Structured RhoGEF recruitment drives myosin II organization on large exocytic vesicles. J Cell Sci, 137(13) PubMed ID: 38899547
Summary:
The Rho family of GTPases plays a crucial role in cellular mechanics by regulating actomyosin contractility through the parallel induction of actin and myosin assembly and function. Using exocytosis of large vesicles in the Drosophila larval salivary gland as a model, the spatiotemporal regulation was followed of Rho1, which in turn creates distinct organization patterns of actin and myosin. After vesicle fusion, low levels of activated Rho1 reach the vesicle membrane and drive actin nucleation in an uneven, spread-out pattern. Subsequently, the Rho1 activator RhoGEF2 distributes as an irregular meshwork on the vesicle membrane, activating Rho1 in a corresponding punctate pattern and driving local myosin II recruitment, resulting in vesicle constriction. Vesicle membrane buckling and subsequent crumpling occur at local sites of high myosin II concentrations. These findings indicate that distinct thresholds for activated Rho1 create a biphasic mode of actomyosin assembly, inducing anisotropic membrane crumpling during exocrine secretion.

Sayeesh, P. M., Iguchi, M., Inomata, K., Ikeya, T., Ito, Y. (2024). Structure and Dynamics of Drk-SH2 Domain and Its Site-Specific Interaction with Sev Receptor Tyrosine Kinase. Int J Mol Sci, 25(12) PubMed ID: 38928093
Summary:
The Drosophila downstream receptor kinase (Drk), a homologue of human GRB2, participates in the signal transduction from the extracellular to the intracellular environment. Drk receives signals through the interaction of its Src homology 2 (SH2) domain with the phosphorylated tyrosine residue in the receptor tyrosine kinases (RTKs). This study presents the solution NMR structure of the SH2 domain of Drk (Drk-SH2), which was determined in the presence of a phosphotyrosine (pY)-containing peptide derived from a receptor tyrosine kinase, Sevenless (Sev). The solution structure of Drk-SH2 possess a common SH2 domain architecture, consisting of three β strands imposed between two α helices. Additionally, the site-specific interactions of the Drk-SH2 domain with the pY-containing peptide was interpreted through NMR titration experiments. The dynamics of Drk-SH2 were also analysed through NMR-relaxation experiments as well as the molecular dynamic simulation. The docking simulations of the pY-containing peptide onto the protein surface of Drk-SH2 provided the orientation of the peptide, which showed a good agreement with the analysis of the SH2 domain of GRB2.

Monday April 14th - Genes, Enzymes and Protein expression, Evolution Structure and Function

Fisher, L. A. B., Carriqui-Madronal, B., Mulder, T., Huelsmann, S., Schock, F., Gonzalez-Morales, N. (2024). Filamin protects myofibrils from contractile damage through changes in its mechanosensory region. PLoS Genet, 20(6):e1011101 PubMed ID: 38905299
Summary:
Filamins are mechanosensitive actin crosslinking proteins that organize the actin cytoskeleton> in a variety of shapes and tissues. In muscles, filamin crosslinks actin filaments from opposing sarcomeres, the smallest contractile units of muscles. This happens at the Z-disc, the actin-organizing center of sarcomeres. In flies and vertebrates, filamin mutations lead to fragile muscles that appear ruptured, suggesting filamin helps counteract muscle rupturing during muscle contractions by providing elastic support and/or through signaling. An elastic region at the C-terminus of filamin is called the mechanosensitive region and has been proposed to sense and counteract contractile damage. This study used molecularly defined mutants and microscopy analysis of the Drosophila indirect flight muscles to investigate the molecular details by which filamin provides cohesion to the Z-disc. Novel filamin mutations affecting the C-terminal region were made to interrogate the mechanosensitive region and detected three Z-disc phenotypes: dissociation of actin filaments, Z-disc rupture, and Z-disc enlargement. A constitutively closed filamin mutant was identified that prevents the elastic changes in the mechanosensitive region and results in ruptured Z-discs, and a constitutively open mutant which has the opposite elastic effect on the mechanosensitive region and gives rise to enlarged Z-discs. Finally, muscle contraction was shown to be required for Z-disc rupture. It is proposed that filamin senses myofibril damage by elastic changes in its mechanosensory region, stabilizes the Z-disc, and counteracts contractile damage at the Z-disc.

Landis, G. N., Bell, H. S., Peng, O. K., Fan, Y., Yan, K., Baybutt, B., Tower, J. (2024). Conditional Inhibition of Eip75B Eliminates the Effects of Mating and Mifepristone on Lifespan in Female Drosophila. Cells, 13(13) PubMed ID: 38994975
Summary:
Mating in female Drosophila melanogaster causes midgut hypertrophy and reduced lifespan, and these effects are blocked by the drug mifepristone. Eip75B is a transcription factor previously reported to have pleiotropic effects on Drosophila lifespan. Because Eip75B null mutations are lethal, conditional systems and/or partial knock-down are needed to study Eip75B effects in adults. Previous studies showed that Eip75B is required for adult midgut cell proliferation in response to mating. To test the possible role of Eip75B in mediating the lifespan effects of mating and mifepristone, a tripartite FLP-recombinase-based conditional system was employed that provides controls for genetic background. Expression of a Hsp70-FLP transgene was induced in third instar larvae by a brief heat pulse. The FLP recombinase catalyzed the recombination and activation of an Actin5C-GAL4 transgene. The GAL4 transcription factor in turn activated expression of a UAS-Eip75B-RNAi transgene. Inhibition of Eip75B activity was confirmed by loss of midgut hypertrophy upon mating, and the lifespan effects of both mating and mifepristone were eliminated. In addition, the negative effects of mifepristone on egg production were eliminated. The data indicate that Eip75B mediates the effects of mating and mifepristone on female midgut hypertrophy, egg production, and lifespan.

Castillo-Mancho, V., Atienza-Manuel, A., Sarmiento-Jimenez, J., Ruiz-Gomez, M., Culi, J. (2024). Phospholipid scramblase 1: an essential component of the nephrocyte slit diaphragm.. Cell Mol Life Sci, 81(1):261 PubMed ID: 38878170
Summary:
Blood ultrafiltration in nephrons critically depends on specialized intercellular junctions between podocytes, named slit diaphragms (SDs). By studying a homologous structure found in Drosophila nephrocytes, this study identified the phospholipid scramblase Scramb1 as an essential component of the SD, uncovering a novel link between membrane dynamics and SD formation. In scramb1 mutants, SDs fail to form. Instead, the SD components Sticks and stones/nephrin, polyhaetoid/ZO-1, and the Src-kinase Src64B/Fyn associate in cortical foci lacking the key SD protein Dumbfounded/NEPH1. Scramb1 interaction with Polychaetoid/ZO-1 and Flotillin2, the presence of essential putative palmitoylation sites and its capacity to oligomerize, suggest a function in promoting SD assembly within lipid raft microdomains. Furthermore, Scramb1 interactors as well as its functional sensitivity to temperature, suggest an active involvement in membrane remodeling processes during SD assembly. Remarkably, putative Ca(2+)-binding sites in Scramb1 are essential for its activity raising the possibility that Ca(2+) signaling may control the assembly of SDs by impacting on Scramb1 activity.

Xu, M., Wu, Z., Li, W., Xue, L. (2024). Gp93 inhibits unfolded protein response-mediated c-Jun N-terminal kinase activation and cell invasion. Journal of cellular physiology, 239(8):e31294 PubMed ID: 38922869
Summary:
In eukaryotes, Hsp90B1 serves as a vital chaperonin, facilitating the accurate folding of proteins. Interestingly, Hsp90B1 exhibits contrasting roles in the development of various types of cancers, although the underlying reasons for this duality remain enigmatic. Through the utilization of the Drosophila model, this study unveils the functional significance of Gp93, the Drosophila ortholog of Hsp90B1, which hitherto had limited reported developmental functions. Employing the Drosophila cell invasion model, the pivotal role of Gp93 in regulating cell invasion and modulating c-Jun N-terminal kinase (JNK) activation were elucidated. Furthermore, this investigation highlights the involvement of the unfolded protein response-associated IRE1/XBP1 pathway in governing Gp93 depletion-induced, JNK-dependent cell invasion. Collectively, these findings not only uncover a novel molecular function of Gp93 in Drosophila, but also underscore a significant consideration pertaining to the testing of Hsp90B1 inhibitors in cancer therapy.

Murthy, S., Dey, U., Olymon, K., Abbas, E., Yella, V. R., Kumar, A. (2024). Discerning the Role of DNA Sequence, Shape, and Flexibility in Recognition by Drosophila Transcription Factors. ACS chemical biology, 19(7):1533-1543 PubMed ID: 38902964
Summary:
The precise spatial and temporal orchestration of gene expression is crucial for the ontogeny of an organism and is mainly governed by transcription factors (TFs). The mechanism of recognition of cognate sites amid millions of base pairs in the genome by TFs is still incompletely understood. This study focuses on DNA sequence composition, shape, and flexibility preferences of 28 quintessential TFs from Drosophila melanogaster that are critical to development and body patterning mechanisms. This study finds that TFs exhibit distinct predilections for DNA shape, flexibility, and sequence compositions in the proximity of transcription factor binding sites (TFBSs). Notably, certain zinc finger proteins prefer GC-rich areas with less negative propeller twist, while homeodomains mainly seek AT-rich regions with a more negative propeller twist at their sites. Intriguingly, while numerous cofactors share similar binding site preferences and bind closer to each other in the genome, some cofactors that have different preferences bind farther apart. These findings shed light on TF DNA recognition and provide novel insights into possible cofactor binding and transcriptional regulation mechanisms.

Bordet, G., Tulin, A. V. (2024).. PARG Protein Regulation Roles in Drosophila Longevity Control. Int J Mol Sci, 25(11) PubMed ID: 38892377
Summary:
Aging, marked by a gradual decline in physiological function and heightened vulnerability to age-related diseases, remains a complex biological process with multifaceted regulatory mechanisms. This study elucidates the critical role of poly(ADP-ribose) glycohydrolase (PARG), responsible for catabolizing poly(ADP-ribose) (pADPr) in the aging process by modulating the expression of age-related genes in Drosophila melanogaster. Specifically, the regulatory function was uncovered of the uncharacterized PARG C-terminal domain in controlling PARG activity. Flies lacking this domain exhibit a significantly reduced lifespan compared to wild-type counterparts. Furthermore, progressive dysregulation of age-related gene expression was observed during aging, accelerated in the absence of PARG activity, culminating in a premature aging phenotype. These findings reveal the critical involvement of the pADPr pathway as a key player in the aging process, highlighting its potential as a therapeutic target for mitigating age-related effects.

Friday, April 11th - RNAs, RNA interference, and Transposons

Chen, P., Pan, K. C., Park, E. H., Luo, Y., Lee, Y. C. G., Aravin, A. A. (2024). Escalation of genome defense capacity enables control of an expanding meiotic driver. bioRxiv, PubMed ID: 38915551
Summary:
rom RNA interference to chromatin silencing, diverse genome defense pathways silence selfish genetic elements to safeguard genome integrity. Despite their diversity, different defense pathways share a modular organization, where numerous specificity factors identify diverse targets and common effectors silence them. In the PIWI-interacting RNA (piRNA) pathway, which controls selfish elements in the metazoan germline, diverse target RNAs are first identified by complementary base pairing with piRNAs and then silenced by PIWI-clade nucleases via enzymatic cleavage. Such a binary architecture allows the defense systems to be readily adaptable, where new targets can be captured via the innovation of new specificity factors. Thus, current understanding of genome defense against lineage-specific selfish genes has been largely limited to the evolution of specificity factors, while it remains poorly understood whether other types of innovations are required. This sttudy describes a new type of innovation, which escalates the defense capacity of the piRNA pathway to control a recently expanded selfish gene in Drosophila melanogaster. Through an in vivo RNAi screen for repressors of Stellate-a recently evolved and expanded selfish meiotic driver-a novel defense factor, Trailblazer, was discovered. Trailblazer is a transcription factor that promotes the expression of two PIWI-clade nucleases, Aub and AGO3, to match Stellate in abundance. Recent innovation in the DNA-binding domain of Trailblazer enabled it to drastically elevate Aub and AGO3 expression in the D. melanogaster lineage, thereby escalating the silencing capacity of the piRNA pathway to control expanded Stellate and safeguard fertility. As copy-number expansion is a recurrent feature of diverse selfish genes across the tree of life, it is envisioned that augmenting the defense capacity to quantitatively match selfish genes is likely a repeatedly employed defense strategy in evolution.

Menzies, J. A. C., Maia Chagas, A., Baden, T., Alonso, C. R. (2024). A microRNA that controls the emergence of embryonic movement. Elife, 13 PubMed ID: 38869942
Summary:
Movement is a key feature of animal systems, yet its embryonic origins are not fully understood. This study investigated the genetic basis underlying the embryonic onset of movement in Drosophila focusing on the role played by small non-coding RNAs (microRNAs, miRNAs). To this end, a quantitative behavioural pipeline capable of tracking embryonic movement in large populations of fly embryos was developed, and uthis system discovered that the Drosophila miRNA miR-2b-1 plays a role in the emergence of movement. Through the combination of spectral analysis of embryonic motor patterns, cell sorting and RNA in situs, genetic reconstitution tests, and neural optical imaging it was found that miR-2b-1 influences the emergence of embryonic movement by exerting actions in the developing nervous system. Furthermore, through the combination of bioinformatics coupled to genetic manipulation of miRNA expression and phenocopy tests a previously uncharacterised (but evolutionarily conserved) chloride channel encoding gene was developed - which was termed Movement Modulator (Motor) - as a genetic target that mechanistically links miR-2b-11 to the onset of movement. Cell-specific genetic reconstitution of miR-2b-1 expression in a null miRNA mutant background, followed by behavioural assays and target gene analyses, suggest that miR-2b-1 affects the emergence of movement through effects in sensory elements of the embryonic circuitry, rather than in the motor domain. This work thus reports the first miRNA system capable of regulating embryonic movement, suggesting that other miRNAs are likely to play a role in this key developmental process in Drosophila as well as in other species.

Duan, Y., Ma, L., Zhao, T., Liu, J., Zheng, C., Song, F., Tian, L., Cai, W., Li, H. (2024). Conserved A-to-I RNA editing with non-conserved recoding expands the candidates of functional editing sites. Fly (Austin), 18(1):2367359 PubMed ID: 38889318
Summary:
Adenosine-to-inosine (A-to-I) RNA editing recodes the genome and confers flexibility for the organisms to adapt to the environment. It is believed that RNA recoding sites are well suited for facilitating adaptive evolution by increasing the proteomic diversity in a temporal-spatial manner. The function and essentiality of a few conserved recoding sites are recognized. However, the experimentally discovered functional sites only make up a small corner of the total sites, and there is still the need to expand the repertoire of such functional sites with bioinformatic approaches. This study defines a new category of RNA editing sites termed 'conserved editing with non-conserved recoding' and systematically identify such sites in Drosophila editomes, figuring out their selection pressure and signals of adaptation at inter-species and intra-species levels. Surprisingly, conserved editing sites with non-conserved recoding are not suppressed and are even slightly overrepresented in Drosophila. DNA mutations leading to such cases are also favoured during evolution, suggesting that the function of those recoding events in different species might be diverged, specialized, and maintained. Finally, structural prediction suggests that such recoding in potassium channel Shab might increase ion permeability and compensate the effect of low temperature. In conclusion, conserved editing with non-conserved recoding might be functional as well. This study provides novel aspects in considering the adaptive evolution of RNA editing sites and meanwhile expands the candidates of functional recoding sites for future validation.

McQuarrie, D. W. J., Alizada, A., Nicholson, B. C., Soller, M. (2024). Rapid evolution of promoters from germline-specifically expressed genes including transposon silencing factors. BMC Genomics, 25(1):678 PubMed ID: 38977960
Summary:
The piRNA pathway in animal gonads functions as an 'RNA-based immune system', serving to silence transposable elements and prevent inheritance of novel invaders. In Drosophila, this pathway relies on three gonad-specific Argonaute proteins (Argonaute-3, Aubergine and Piwi) that associate with 23-28 nucleotide piRNAs, directing the silencing of transposon-derived transcripts. Transposons constitute a primary driver of genome evolution, yet the evolution of piRNA pathway factors has not received in-depth exploration. Specifically, channel nuclear pore proteins, which impact piRNA processing, exhibit regions of rapid evolution in their promoters. Consequently, the question arises whether such a mode of evolution is a general feature of transposon silencing pathways. By employing genomic analysis of coding and promoter regions within genes that function in transposon silencing in Drosophila, this study demonstrated that the promoters of germ cell-specific piRNA factors are undergoing rapid evolution. These findings indicate that rapid promoter evolution is a common trait among piRNA factors engaged in germline silencing across insect species, potentially contributing to gene expression divergence in closely related taxa. Furthermore, it was observed that the promoters of genes exclusively expressed in germ cells generally exhibit rapid evolution, with some divergence in gene expression. These results suggest that increased germline promoter evolution, in partnership with other factors, could contribute to transposon silencing and evolution of species through differential expression of genes driven by invading transposons.

Teng, Z., Yang, L., Zhang, Q., Chen, Y., Wang, X., Zheng, Y., Tian, A., Tian, D., Lin, Z., Deng, W. M., Liu, H. (2024). Topoisomerase I is an evolutionarily conserved key regulator for satellite DNA transcription. Nat Commun, 15(1):5151 PubMed ID: 38886382
Summary:
RNA Polymerase (RNAP) II transcription on non-coding repetitive satellite DNAs plays an important role in chromosome segregation, but a little is known about the regulation of satellite transcription. This study shows that Topoisomerase I (TopI), not TopII, promotes the transcription of α-satellite DNAs, the main type of satellite DNAs on human centromeres. Mechanistically, TopI localizes to centromeres, binds RNAP II and facilitates RNAP II elongation. Interestingly, in response to DNA double-stranded breaks (DSBs), α-satellite transcription is dramatically stimulated in a DNA damage checkpoint-independent but TopI-dependent manner, and these DSB-induced α-satellite RNAs form into strong speckles in the nucleus. Remarkably, TopI-dependent satellite transcription also exists in mouse 3T3 and Drosophila S2 cells and in Drosophila larval imaginal wing discs and tumor tissues. Altogether, these findings reveal an evolutionally conserved mechanism with TopI as a key player for the regulation of satellite transcription at both cellular and animal levels.

Stewart, R. K., Nguyen, P., Laederach, A., Volkan, P. C., Sawyer, J. K., Fox, D. T. (2024). Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation. Nat Commun, 15(1):5270 PubMed ID: 38902233
Summary:
Regulation of codon optimality is an increasingly appreciated layer of cell- and tissue-specific protein expression control. Here, we use codon-modified reporters to show that differentiation of Drosophila neural stem cells into neurons enables protein expression from rare-codon-enriched genes. From a candidate screen, this study identified the cytoplasmic polyadenylation element binding (CPEB) protein Orb2 as a positive regulator of rare-codon-dependent mRNA stability in neurons. Using RNA sequencing, Orb2-upregulated mRNAs were revealed in the brain with abundant Orb2 binding sites have a rare-codon bias. From these Orb2-regulated mRNAs, rare-codon enrichment was demonstrated to be important for mRNA stability and social behavior function of the metabotropic glutamate receptor (mGluR). These findings reveal a molecular mechanism by which neural stem cell differentiation shifts genetic code regulation to enable critical mRNA stability and protein expression.

Wednesday, April 9th - Adult neural structure, development and function

Medeiros, A. M., Hobbiss, A. F., Borges, G., Moita, M., Mendes, C. S. (2024). Mechanosensory bristles mediate avoidance behavior by triggering sustained local motor activity in Drosophila melanogaster. Curr Biol, 34(13):2812-2830. PubMed ID: 38861987
Summary:
During locomotion, most vertebrates-and invertebrates such as Drosophila melanogaster-are able to quickly adapt to terrain irregularities or avoid physical threats by integrating sensory information along with motor commands. Key to this adaptability are leg mechanosensory structures, which assist in motor coordination by transmitting external cues and proprioceptive information to motor centers in the central nervous system. Nevertheless, how different mechanosensory structures engage these locomotor centers remains poorly understood. This study tested the role of mechanosensory structures in movement initiation by optogenetically stimulating specific classes of leg sensory structures. This study found that stimulation of leg mechanosensory bristles (MsBs) and the femoral chordotonal organ (ChO) is sufficient to initiate forward movement in immobile animals. While the stimulation of the ChO required brain centers to induce forward movement, unexpectedly, brief stimulation of leg MsBs triggered a fast response and sustained motor activity dependent only on the ventral nerve cord (VNC). Moreover, this leg-MsB-mediated movement lacked inter- and intra-leg coordination but preserved antagonistic muscle activity within joints. Finally, leg-MsB activation was shown to mediate strong avoidance behavior away from the stimulus source, which is preserved even in the absence of a central brain. Overall, these data show that mechanosensory stimulation can elicit a fast motor response, independently of central brain commands, to evade potentially harmful stimuli. In addition, it sheds light on how specific sensory circuits modulate motor control, including initiation of movement, allowing a better understanding of how different levels of coordination are controlled by the VNC and central brain locomotor circuits.

Smolin, N., Dombrovski, M., Hina, B. W., Moreno-Sanchez, A., Gossart, R., Carmona, C. R., Rehan, A., Hussein, R. H., Mirshahidi, P., Ausborn, J., Kurmangaliyev, Y. Z., von Reyn, C. R. (2024). Neuronal identity control at the resolution of a single transcription factor isoform. bioRxiv, PubMed ID: 38915533
Summary:
The brain exhibits remarkable neuronal diversity which is critical for its functional integrity. From the sheer number of cell types emerging from extensive transcriptional, morphological, and connectome datasets, the question arises of how the brain is capable of generating so many unique identities. "Terminal selectors" are transcription factors hypothesized to determine the final identity characteristics in post-mitotic cells. Which transcription factors function as terminal selectors and the level of control they exert over different terminal characteristics are not well defined. This study establish a novel role for the transcription factor broad as a terminal selector in Drosophila melanogaster. This study capitalized on existing large sequencing and connectomics datasets and employ a comprehensive characterization of terminal characteristics including Perturb-seq and whole-cell electrophysiology. A single isoform Broad-z4 was found to serve as the switch between the identity of two visual projection neurons LPLC1 and LPLC2. Broad-z4 is natively expressed in LPLC1, and is capable of transforming the transcriptome, morphology, and functional connectivity of LPLC2 cells into LPLC1 cells when perturbed. This comprehensive work establishes a single isoform as the smallest unit underlying an identity switch, which may serve as a conserved strategy replicated across developmental programs.

Syed, D. S., Ravbar, P., Simpson, J. H. (2024). Inhibitory circuits generate rhythms for leg movements during Drosophila grooming. bioRxiv, PubMed ID: 38895414
Summary:
Limbs execute diverse actions coordinated by the nervous system through multiple motor programs. The basic architecture of motor neurons that activate muscles that articulate joints for antagonistic flexion and extension movements is conserved from flies to vertebrates. While excitatory premotor circuits are expected to establish sets of leg motor neurons that work together, this study uncovered a new instructive role for inhibitory circuits: their ability to generate rhythmic leg movements. Using electron microscopy data for the Drosophila nerve cord, ~120 GABAergic inhibitory neurons were categorized from the 13A and 13B hemi-lineages into classes based on similarities in morphology and connectivity. By mapping their synaptic partners, pathways were uncovered for inhibiting specific groups of motor neurons, disinhibiting antagonistic counterparts, and inducing alternation between flexion and extension. The function of specific inhibitory neurons was tested through optogenetic activation and silencing, using an in-depth ethological analysis of leg movements during grooming. Anatomy and behavior analysis findings were combined to construct a computational model that can reproduce major aspects of the observed behavior, confirming the sufficiency of these premotor inhibitory circuits to generate rhythms.

Lesser, E., Azevedo, A. W., Phelps, J. S., Elabbady, L., Cook, A., Syed, D. S., Mark, B., Kuroda, S., Sustar, A., Moussa, A., Dallmann, C. J., Agrawal, S., Lee, S. J., Pratt, B., Skutt-Kakaria, K., Gerhard, S., Lu, R., Kemnitz, N., Lee, K., Halageri, A., Castro, M., Ih, D., Gager, J., Tammam, M., Dorkenwald, S., Collman, F., Schneider-Mizell, C., Brittain, D., Jordan, C. S., Macrina, T., Dickinson, M., Lee, W. A., Tuthill, J. C. (2024). Synaptic architecture of leg and wing premotor control networks in Drosophila. Nature, 631(8020):369-377 PubMed ID: 38926579
Summary:
Animal movement is controlled by motor neurons (MNs), which project out of the central nervous system to activate muscles. MN activity is coordinated by complex premotor networks that facilitate the contribution of individual muscles to many different behaviours. This study used connectomics to analyse the wiring logic of premotor circuits controlling the Drosophila leg and wing. We find that both premotor networks cluster into modules that link MNs innervating muscles with related functions. Within most leg motor modules, the synaptic weights of each premotor neuron are proportional to the size of their target MNs, establishing a circuit basis for hierarchical MN recruitment. By contrast, wing premotor networks lack proportional synaptic connectivity, which may enable more flexible recruitment of wing steering muscles. Through comparison of the architecture of distinct motor control systems within the same animal, common principles were identified of premotor network organization and specializations that reflect the unique biomechanical constraints and evolutionary origins of leg and wing motor control.

Chu, S. Y., Lai, Y. W., Hsu, T. C., Lu, T. M., Yu, H. H. (2024). Isoforms of terminal selector Mamo control axon guidance during adult Drosophila memory center construction via Semaphorin-1a. Dev Biol, 515:1-6 PubMed ID: 38906235
Summary:
In animals undergoing metamorphosis, the appearance of the nervous system is coincidently transformed by the morphogenesis of neurons. Such morphogenic alterations are exemplified in three types of intrinsic neurons in the Drosophila memory center. In contrast to the well-characterized remodeling of γ neurons, the morphogenesis of αβ and α'/β' neurons has not been adequately explored. Here, we show that mamo, a BTB-zinc finger transcription factor that acts as a terminal selector for α'/β' neurons, controls the formation of the correct axonal pattern of α'/β' neurons. Intriguingly, specific Mamo isoforms are preferentially expressed in α'/β' neurons to regulate the expression of axon guidance molecule Semaphorin-1a. This action directs proper axon guidance in α'/β' neurons, which is also crucial for wiring of α'/β' neurons with downstream neurons. Taken together, these results provide molecular insights into how neurons establish correct axonal patterns in circuitry assembly during adult memory center construction.

Turrel, O., Gao, L., Sigrist, S. J. (2024). Presynaptic regulators in memory formation. Learn Mem, 31(5) PubMed ID: 38862173
Summary:
The intricate molecular and structural sequences guiding the formation and consolidation of memories within neuronal circuits remain largely elusive. This study investigated the roles of two pivotal presynaptic regulators, the small GTPase Rab3, enriched at synaptic vesicles, and the cell adhesion protein Neurexin-1, in the formation of distinct memory phases within the Drosophila mushroom body Kenyon cells. These findings suggest that both proteins play crucial roles in memory-supporting processes within the presynaptic terminal, operating within distinct plasticity modules. These modules likely encompass remodeling and maturation of existing active zones (AZs), as well as the formation of new AZs.

Monday, April 7th - Tumor Models in Drosophila

Church, S. J., Pulianmackal, A. J., Dixon, J. A., Loftus, L. V., Amend, S. R., Pienta, K., Cackowski, F. C., Buttitta, L. A. (2024). Oncogenic signaling in the adult Drosophila prostate-like accessory gland leads to activation of a conserved pro-tumorigenic program, in the absence of proliferation. bioRxiv, PubMed ID: 38853988
Summary:
Drosophila models for tumorigenesis and metastasis have revealed conserved mechanisms of signaling that are also involved in mammalian cancer. Many of these models use the proliferating tissues of the larval stages of Drosophila development, when tissues are highly mitotically active, or stem cells are abundant. Fewer Drosophila tumorigenesis models use adult animals to initiate tumor formation when many tissues are largely terminally differentiated and postmitotic. The Drosophila accessory glands are prostate-like tissues and a model for some aspects of prostate tumorigenesis using this tissue has been explored. In this model, oncogenic signaling was induced during the proliferative stage of accessory gland development, raising the question of how oncogenic activity would impact the terminally differentiated and postmitotic adult tissue. Oncogenic signaling in the adult Drosophila accessory gland was shown to lead to activation of a conserved pro-tumorigenic program, similar to that observed in mitotic larval tissues, but in the absence of proliferation. Oncogenic signaling in the adult postmitotic gland leads to tissue hyperplasia with nuclear anaplasia and aneuploidy through endoreduplication, which increases polyploidy and occasionally results in non-mitotic neoplastic-like extrusions. Gene expression changes in the Drosophila model were compared with that of endocycling prostate cancer cells induced by chemotherapy, which potentially mediate tumor recurrence after treatment. Similar signaling pathways are activated in the Drosophila gland and endocycling cancer cells, suggesting the adult accessory glands provide a useful model for aspects of prostate cancer progression that do not involve cellular proliferation.

Pilesi, E., Tesoriere, G., Ferriero, A., Mascolo, E., Liguori, F., Argiro, L., Angioli, C., Tramonti, A., Contestabile, R., Volonte, C., Verni, F. (2024). Vitamin B6 deficiency cooperates with oncogenic Ras to induce malignant tumors in Drosophila. Cell Death Dis, 15(6):388 PubMed ID: 38830901
Summary:
Vitamin B6 is a water-soluble vitamin which possesses antioxidant properties. Its catalytically active form, pyridoxal 5'-phosphate (PLP), is a crucial cofactor for DNA and amino acid metabolism. The inverse correlation between vitamin B6 and cancer risk has been observed in several studies, although dietary vitamin B6 intake sometimes failed to confirm this association. However, the molecular link between vitamin B6 and cancer remains elusive. Previous work has shown that vitamin B6 deficiency causes chromosome aberrations (CABs) in Drosophila and human cells, suggesting that genome instability may correlate the lack of this vitamin to cancer. This study provides evidence in support of this hypothesis. Firstly, PLP deficiency, induced by the PLP antagonists 4-deoxypyridoxine (4DP) or ginkgotoxin (GT), was shown to promote tumorigenesis in eye larval discs transforming benign Ras^V12 tumors into aggressive forms. In contrast, PLP supplementation reduced the development of tumors. Low PLP levels, induced by 4DP or by silencing the sgll(PNPO) gene involved in PLP biosynthesis, worsened the tumor phenotype in another Drosophila cancer model generated by concomitantly activating Ras^V12 and downregulating Discs-large (Dlg) gene. Moreover, Ras(V12) eye discs from larvae reared on 4DP displayed CABs, reactive oxygen species (ROS) and low catalytic activity of serine hydroxymethyltransferase (SHMT), a PLP-dependent enzyme involved in thymidylate (dTMP) biosynthesis, in turnRRQrfrebbbgg required for DNA replication and repair. Feeding Ras(V12) 4DP-fed larvae with PLP or ascorbic acid (AA) plus dTMP, rescued both CABs and tumors. The same effect was produced by overexpressing catalase in Ras(V12) Dlg(RNAi) 4DP-fed larvae, thus allowing to establish a relationship between PLP deficiency, CABs, and cancer. Overall, these data provide the first in vivo demonstration that PLP deficiency can impact on cancer by increasing genome instability, which is in turn mediated by ROS and reduced dTMP levels.

Vialat, M., Baabdaty, E., Trousson, A., Kocer, A., Lobaccaro, J. A., Baron, S., Morel, L., de Joussineau, C. (2024). Cholesterol Dietary Intake and Tumor Cell Homeostasis Drive Early Epithelial Tumorigenesis: A Potential Modelization of Early Prostate Tumorigenesis. JCancers, 16(11) PubMed ID: 38893271
Summary:
Epidemiological studies point to cholesterol as a possible key factor for both prostate cancer incidence and progression. It could represent a targetable metabolite as the most aggressive tumors also appear to be sensitive to therapies designed to decrease hypercholesterolemia, such as statins. However, it remains unknown whether and how cholesterol, through its dietary uptake and its metabolism, could be important for early tumorigenesis. Oncogene clonal induction in the Drosophila melanogaster accessory gland allows reproduction of tumorigenesis from initiation to early progression, where tumor cells undergo basal extrusion to form extra-epithelial tumors. These tumors accumulate lipids, and especially esterified cholesterol, as in human late carcinogenesis. Interestingly, a high-cholesterol diet has a limited effect on accessory gland tumorigenesis. On the contrary, cell-specific downregulation of cholesterol uptake, intracellular transport, or metabolic response impairs the formation of such tumors. Furthermore, in this context, a high-cholesterol diet suppresses this impairment. Interestingly, expression data from primary prostate cancer tissues indicate an early signature of redirection from cholesterol de novo synthesis to uptake. Taken together, these results reveal that during early tumorigenesis, tumor cells strongly increase their uptake and use of dietary cholesterol to specifically promote the step of basal extrusion. Hence, these results suggest the mechanism by which a reduction in dietary cholesterol could lower the risk and slow down the progression of prostate cancer.

Leung, N. Y., Xu, C., Li, J. S. S., Ganguly, A., Meyerhof, G. T., Regimbald-Dumas, Y., Lane, E. A., Breault, D. T., He, X., Perrimon, N., Montell, C. (2024). Gut tumors in flies alter the taste valence of an anti-tumorigenic bitter compound.. Curr Biol, 34(12):2623-2632 PubMed ID: 38823383
Summary:
The sense of taste is essential for survival, as it allows animals to distinguish between foods that are nutritious from those that are toxic. However, innate responses to different tastants can be modulated or even reversed under pathological conditions. This study examined whether and how the internal status of an animal impacts taste valence by using Drosophila models of hyperproliferation in the gut. In all three models where proliferation-inducing transgenes were expressed in intestinal stem cells (ISCs), hyperproliferation of ISCs caused a tumor-like phenotype in the gut. While tumor-bearing flies had no deficiency in overall food intake, strikingly, they exhibited an increased gustatory preference for aristolochic acid (ARI), which is a bitter and normally aversive plant-derived chemical. ARI had anti-tumor effects in all three gut hyperproliferation models. For other aversive chemicals tested that are bitter but do not have anti-tumor effects, gut tumors did not affect avoidance behaviors. Bitter-sensing gustatory receptor neurons (GRNs) in tumor-bearing flies respond normally to ARI. Therefore, the internal pathology of gut hyperproliferation affects neural circuits that determine taste valence postsynaptic to GRNs rather than altering taste identity by GRNs. Overall, these data suggest that increased consumption of ARI may represent an attempt at self-medication. Finally, although ARI's potential use as a chemotherapeutic agent is limited by its known toxicity in the liver and kidney, these findings suggest that tumor-bearing flies might be a useful animal model to screen for novel anti-tumor drugs (Leung, 2024).

Rawal, C. C., Loubiere, V., Butova, N. L., Gracia, J., Parreno, V., Merigliano, C., Martinez, A. M., Cavalli, G., Chiolo, I. (2024). Sustained inactivation of the Polycomb PRC1 complex induces DNA repair defects and genomic instability in epigenetic tumors. Histochemistry and cell biology, 162(1-2):133-147 PubMed ID: 38888809
Summary:

Cancer initiation and progression are typically associated with the accumulation of driver mutations and genomic instability. However, recent studies demonstrated that cancer can also be driven purely by epigenetic alterations, without driver mutations. Specifically, a 24-h transient downregulation of polyhomeotic (ph-KD), a core component of the Polycomb complex PRC1, is sufficient to induce epigenetically initiated cancers (EICs) in Drosophila, which are proficient in DNA repair and characterized by a stable genome. Whether genomic instability eventually occurs when PRC1 downregulation is performed for extended periods of time remains unclear. This study shows that prolonged depletion of PH, which mimics cancer initiating events, results in broad dysregulation of DNA replication and repair genes, along with the accumulation of DNA breaks, defective repair, and widespread genomic instability in the cancer tissue. A broad misregulation of H2AK118 ubiquitylation and to a lesser extent of H3K27 trimethylation also occurs and might contribute to these phenotypes. Together, this study supports a model where DNA repair and replication defects accumulate during the tumorigenic transformation epigenetically induced by PRC1 loss, resulting in genomic instability and cancer progression.

Parreno, V., Loubiere, V., Schuettengruber, B., Fritsch, L., Rawal, C. C., Erokhin, M., Gyorffy, B., Normanno, D., Di Stefano, M., Moreaux, J., Butova, N. L., Chiolo, I., Chetverina, D., Martinez, A. M., Cavalli, G. (2024). Transient loss of Polycomb components induces an epigenetic cancer fate. Nature, 629(8012):688-696 PubMed ID: 38658752
Summary:
Although cancer initiation and progression are generally associated with the accumulation of somatic mutations, substantial epigenomic alterations underlie many aspects of tumorigenesis and cancer susceptibility, suggesting that genetic mechanisms might not be the only drivers of malignant transformation. However, whether purely non-genetic mechanisms are sufficient to initiate tumorigenesis irrespective of mutations has been unknown. This study shows that a transient perturbation of transcriptional silencing mediated by Polycomb group proteins is sufficient to induce an irreversible switch to a cancer cell fate in Drosophila. This is linked to the irreversible derepression of genes that can drive tumorigenesis, including members of the JAK-STAT signalling pathway and zfh1, the fly homologue of the ZEB1 oncogene, whose aberrant activation is required for Polycomb perturbation-induced tumorigenesis. These data show that a reversible depletion of Polycomb proteins can induce cancer in the absence of driver mutations, suggesting that tumours can emerge through epigenetic dysregulation leading to inheritance of altered cell fates (Parreno, 2024).

Friday, April 4th - Larval and Adult Development

Blackie, L., Gaspar, P., Mosleh, S., Lushchak, O., Kong, L., Jin, Y., Zielinska, A. P., Cao, B., Mineo, A., Silva, B., Ameku, T., Lim, S. E., Mao, Y., Prieto-Godino, L., Schoborg, T., Varela, M., Mahadevan, L., Miguel-Aliaga, I. (2024). The sex of organ geometry. Nature, 630(8016):392-400 PubMed ID: 38811741
Summary:
Organs have a distinctive yet often overlooked spatial arrangement in the body. It is proposed that there is a logic to the shape of an organ and its proximitY to its neighbours. Here, by using volumetric scans of many Drosophila melanogaster flies, we develop methods to quantify three-dimensional features of organ shape, position and interindividual variability. Both the shapes of organs and their relative arrangement were consistent yet differ between the sexes, and identify unexpected interorgan adjacencies and left-right organ asymmetries. Focusing on the intestine, which traverses the entire body, this study investigate how sex differences in three-dimensional organ geometry arise. The configuration of the adult intestine is only partially determined by physical constraints imposed by adjacent organs; its sex-specific shape is actively maintained by mechanochemical crosstalk between gut muscles and vascular-like trachea. Indeed, sex-biased expression of a muscle-derived fibroblast growth factor-like ligand renders trachea sexually dimorphic. In turn, tracheal branches hold gut loops together into a male or female shape, with physiological consequences. Interorgan geometry represents a previously unrecognized level of biological complexity which might enable or confine communication across organs and could help explain sex or species differences in organ function.

Rigato, A., Meng, H., Chardes, C., Runions, A., Abouakil, F., Smith, R. S., LeGoff, L. (2024). A mechanical transition from tension to buckling underlies the jigsaw puzzle shape morphogenesis of histoblasts in the Drosophila epidermis. PLoS Biol, 22(6):e3002662 PubMed ID: 38870210
Summary:
The polygonal shape of cells in proliferating epithelia is a result of the tensile forces of the cytoskeletal cortex and packing geometry set by the cell cycle. In the larval Drosophila epidermis, two cell populations, histoblasts and larval epithelial cells, compete for space as they grow on a limited body surface. They do so in the absence of cell divisions. A striking morphological transition of histoblasts was observed during larval development, where they change from a tensed network configuration with straight cell outlines at the level of adherens junctions to a highly folded morphology. The apical surface of histoblasts shrinks while their growing adherens junctions fold, forming deep lobules. Volume increase of growing histoblasts is accommodated basally, compensating for the shrinking apical area. The folded geometry of apical junctions resembles elastic buckling, and the imbalance between the shrinkage of the apical domain of histoblasts and the continuous growth of junctions triggers buckling. This model is supported by laser dissections and optical tweezer experiments together with computer simulations. This analysis pinpoints the ability of histoblasts to store mechanical energy to a much greater extent than most other epithelial cell types investigated so far, while retaining the ability to dissipate stress on the hours time scale. Finally, a possible mechanism is proposed for size regulation of histoblast apical size through the lateral pressure of the epidermis, driven by the growth of cells on a limited surface. Buckling effectively compacts histoblasts at their apical plane and may serve to avoid physical harm to these adult epidermis precursors during larval life. This work indicates that in growing nondividing cells, compressive forces, instead of tension, may drive cell morphology.

Petrosky, S. J., Williams, T. M., Rebeiz, M. (2024). A genetic screen of transcription factors in the Drosophila melanogaster abdomen identifies novel pigmentation genes. G3 (Bethesda), 14(9) PubMed ID: 38820091
Summary:
Gene regulatory networks specify the gene expression patterns needed for traits to develop. Differences in these networks can result in phenotypic differences between organisms. Although loss-of-function genetic screens can identify genes necessary for trait formation, gain-of-function screens can overcome genetic redundancy and identify loci whose expression is sufficient to alter trait formation. Here, we leveraged transgenic lines from the Transgenic RNAi Project at Harvard Medical School to perform both gain- and loss-of-function CRISPR/Cas9 screens for abdominal pigmentation phenotypes. Measurable effects on pigmentation patterns in the Drosophila melanogaster abdomen were observed for 21 of 55 transcription factors in gain-of-function experiments and 7 of 16 tested by loss-of-function experiments. These included well-characterized pigmentation genes, such as bab1 and dsx, and transcription factors that had no known role in pigmentation, such as slp2. Finally, this screen was partially conducted by undergraduate students in a Genetics Laboratory course during the spring semesters of 2021 and 2022. This screen was found to be a successful model for student engagement in research in an undergraduate laboratory course that can be readily adapted to evaluate the effect of hundreds of genes on many different Drosophila traits, with minimal resources.

Kurogi, Y., Mizuno, Y., Kamiyama, T., Niwa, R. (2024). The intestinal stem cell/enteroblast-GAL4 driver, escargot-GAL4, also manipulates gene expression in the juvenile hormone-synthesizing organ of Drosophila melanogaster. Sci Rep, 14(1):9631 PubMed ID: 38671036
Summary:
Intestinal stem cells (ISCs) of the fruit fly, Drosophila melanogaster, offer an excellent genetic model to explore homeostatic roles of ISCs in animal physiology. Among available genetic tools, the escargot (esg)-GAL4 driver, expressing the yeast transcription factor gene, GAL4, under control of the esg gene promoter, has contributed significantly to ISC studies. This driver facilitates activation of genes of interest in proximity to a GAL4-binding element, Upstream Activating Sequence, in ISCs and progenitor enteroblasts (EBs). While esg-GAL4 has been considered an ISC/EB-specific driver, recent studies have shown that esg-GAL4 is also active in other tissues, such as neurons and ovaries. Therefore, the ISC/EB specificity of esg-GAL4 is questionable. This study reveals esg-GAL4 expression in the corpus allatum (CA), responsible for juvenile hormone (JH) production. When driving the oncogenic gene, Ras(V12), esg-GAL4 induces overgrowth in ISCs/EBs as reported, but also increases CA cell number and size. Consistent with this observation, animals alter expression of JH-response genes. These data show that esg-GAL4-driven gene manipulation can systemically influence JH-mediated animal physiology, arguing for cautious use of esg-GAL4 as a "specific" ISC/EB driver to examine ISC/EB-mediated animal physiology.

Raja, K. K. B., Yeung, K., Li, Y., Chen, R., Mardon, G. (2024). A single cell RNA sequence atlas of the early Drosophila larval eye. BMC Genomics, 25(1):616 PubMed ID: 38890587
Summary:
The Drosophila eye has been an important model to understand principles of differentiation, proliferation, apoptosis and tissue morphogenesis. However, a single cell RNA sequence resource that captures gene expression dynamics from the initiation of differentiation to the specification of different cell types in the larval eye disc is lacking. This study reports transcriptomic data from 13,000 cells that cover six developmental stages of the larval eye. The data show cell clusters that correspond to all major cell types present in the eye disc ranging from the initiation of the morphogenetic furrow to the differentiation of each photoreceptor cell type as well as early cone cells. We identify dozens of cell type-specific genes whose function in different aspects of eye development have not been reported. These single cell data will greatly aid research groups studying different aspects of early eye development and will facilitate a deeper understanding of the larval eye as a model system.

Ray, A., Rai, Y., Inamdar, M. S. (2024). The Endosomal Sorting Complex, ESCRT, has diverse roles in blood progenitor maintenance, lineage choice and immune response. Biol Open, 13(6) PubMed ID: 38828842
Summary:
Most hematological malignancies are associated with reduced expression of one or more components of the Endosomal Sorting Complex Required for Transport (ESCRT). However, the roles of ESCRT in stem cell and progenitor maintenance are not resolved. Parsing signaling pathways in relation to the canonical role of ESCRT poses a challenge. The Drosophila hematopoietic organ, the larval lymph gland, provides a path to dissect the roles of cellular trafficking pathways such as ESCRT in blood development and maintenance. Drosophila has 13 core ESCRT components. Knockdown of individual ESCRTs showed that only Vps28 and Vp36 were required in all lymph gland progenitors. Using the well-conserved ESCRT-II complex as an example of the range of phenotypes seen upon ESCRT depletion, this study showed that ESCRTs have cell-autonomous as well as non-autonomous roles in progenitor maintenance and differentiation. ESCRT depletion also sensitized posterior lobe progenitors to respond to immunogenic wasp infestation. Key heterotypic roles for ESCRT have been found in position-dependent control of Notch activation to suppress crystal cell differentiation. This study shows that the cargo sorting machinery determines the identity of progenitors and their adaptability to the dynamic microenvironment. These mechanisms for control of cell fate may tailor developmental diversity in multiple contexts.

Thursday, April 3rd - Disease Models

Gunasekaran, M., Littel, H. R., Wells, N. M., Turner, J., Campos, G., Venigalla, S., Estrella, E. A., Ghosh, P. S., Daugherty, A. L., Stafki, S. A., Kunkel, L. M., Foley, A. R., Donkervoort, S., Bonnemann, C. G., Toledo-Bravo de Laguna, L., Nascimento, A., Benito, D. N., Draper, I., Bruels, C. C., Pacak, C. A., Kang, P. B. (2024). Effects of HMGCR deficiency on skeletal muscle development. bioRxiv, PubMed ID: 38903061
Summary:
Pathogenic variants in HMGCR were recently linked to a limb-girdle muscular dystrophy (LGMD) phenotype. The protein product HMG CoA reductase (HMGCR) catalyzes a key component of the cholesterol synthesis pathway. The two other muscle diseases associated with HMGCR, statin-associated myopathy (SAM) and autoimmune anti-HMGCR myopathy, are not inherited in a Mendelian pattern. The mechanism linking pathogenic variants in HMGCR with skeletal muscle dysfunction is unclear. This study knocked down Hmgcr in mouse skeletal myoblasts, knocked down hmgcr in Drosophila, and expressed three pathogenic HMGCR variants (c.1327C>T, p.Arg443Trp; c.1522_1524delTCT, p.Ser508del; and c.1621G>A, p.Ala541Thr) in Hmgcr knockdown mouse myoblasts. Hmgcr deficiency was associated with decreased proliferation, increased apoptosis, and impaired myotube fusion. Transcriptome sequencing of Hmgcr knockdown versus control myoblasts revealed differential expression involving mitochondrial function, with corresponding differences in cellular oxygen consumption rates. Both ubiquitous and muscle-specific knockdown of hmgcr in Drosophila led to lethality. Overexpression of reference HMGCR cDNA rescued myotube fusion in knockdown cells, whereas overexpression of the pathogenic variants of HMGCR cDNA did not. These results suggest that the three HMGCR-related muscle diseases share disease mechanisms related to skeletal muscle development.

Zuniga, G., Katsumura, S., De Mange, J., Ramirez, P., Atrian, F., Morita, M., Frost, B. (2024). Pathogenic tau induces an adaptive elevation in mRNA translation rate at early stages of disease. Aging Cell:e14245 PubMed ID: 38932463
Summary:
Alterations in the rate and accuracy of messenger RNA (mRNA) translation are associated with aging and several neurodegenerative disorders, including Alzheimer's disease and related tauopathies. Previous work showed that error-containing RNA that are normally cleared via nonsense-mediated mRNA decay (NMD), a key RNA surveillance mechanism, are translated in the adult brain of a Drosophila model of tauopathy. The current study found that newly-synthesized peptides and translation machinery accumulate within nuclear envelope invaginations that occur as a consequence of tau pathology, and that the rate of mRNA translation is globally elevated in early stages of disease in adult brains of Drosophila models of tauopathy. Polysome profiling from adult heads of tau transgenic Drosophila reveals the preferential translation of specific mRNA that have been previously linked to neurodegeneration. Unexpectedly, this study found that panneuronal elevation of NMD further elevates the global translation rate in tau transgenic Drosophila, as does treatment with rapamycin. As NMD activation and rapamycin both suppress tau-induced neurodegeneration, their shared effect on translation suggests that elevated rates of mRNA translation are an early adaptive mechanism to limit neurodegeneration. This work provides compelling evidence that tau-induced deficits in NMD reshape the tau translatome by increasing translation of RNA that are normally repressed in healthy cells.

Deb, W., Rosenfelt, C., Vignard, V., Papendorf, J. J., ...., McWalter, K., Lupski, J. R., Isidor, B., Bolduc, F. V., Bezieau, S., Kruger, E., Kury, S., Ebstein, F. (2024). PSMD11 loss-of-function variants correlate with a neurobehavioral phenotype, obesity, and increased interferon response. American journal of human genetics, 111(7):1352-1369 PubMed ID: 38866022
Summary:
Primary proteasomopathies have recently emerged as a new class of rare early-onset neurodevelopmental disorders (NDDs) caused by pathogenic variants in the PSMB1, PSMC1, PSMC3, or PSMD12 proteasome genes. Proteasomes are large multi-subunit protein complexes that maintain cellular protein homeostasis by clearing ubiquitin-tagged damaged, misfolded, or unnecessary proteins. In this study, this study have identified PSMD11 as an additional proteasome gene in which pathogenic variation is associated with an NDD-causing proteasomopathy. PSMD11 loss-of-function variants caused early-onset syndromic intellectual disability and neurodevelopmental delay with recurrent obesity in 10 unrelated children. These findings demonstrate that the cognitive impairment observed in these individuals could be recapitulated in Drosophila melanogaster with depletion of the PMSD11 ortholog Rpn6, which compromised reversal learning. Investigations in subject samples further revealed that PSMD11 loss of function resulted in impaired 26S proteasome assembly and the acquisition of a persistent type I interferon (IFN) gene signature, mediated by the integrated stress response (ISR) protein kinase R (PKR). In summary, these data identify PSMD11 as an additional member of the growing family of genes associated with neurodevelopmental proteasomopathies and provide insights into proteasomal biology in human health.

Stojkovic, M., Petrovic, M., Capovilla, M., Milojevic, S., Makevic, V., Budimirovic, D. B., Corscadden, L., He, S., Protic, D. (2024). Using a Combination of Novel Research Tools to Understand Social Interaction in the Drosophila melanogaster Model for Fragile X Syndrome. Biology, 13(6) PubMed ID: 38927312
Summary:
Fragile X syndrome (FXS), the most common monogenic cause of inherited intellectual disability and autism spectrum disorder, is caused by a full mutation (>200 CGG repeats) in the Fragile X Messenger Ribonucleoprotein 1 (FMR1) gene. Individuals with FXS experience various challenges related to social interaction (SI). Animal models, such as the Drosophila melanogaster model for FXS where the only ortholog of human FMR1 (dFMR1) is mutated, have played a crucial role in the understanding of FXS. The aim of this study was to investigate SI in the dFMR1^B55 mutants (the groups of flies of both sexes simultaneously) using the novel Drosophila Shallow Chamber and a Python data processing pipeline based on social network analysis (SNA). In comparison with wild-type flies (w(1118)), SNA analysis in dFMR1^B55 mutants revealed hypoactivity, fewer connections in their networks, longer interaction duration, a lower ability to transmit information efficiently, fewer alternative pathways for information transmission, a higher variability in the number of interactions they achieved, and flies tended to stay near the boundaries of the testing chamber. These observed alterations indicate the presence of characteristic strain-dependent social networks in dFMR1^B55 flies, commonly referred to as the group phenotype. Finally, combining novel research tools is a valuable method for SI research in fruit flies.

Sujkowski, A., Ranxhi, B., Bangash, Z. R., Chbihi, Z. M., Prifti, M. V., Qadri, Z., Alam, N., Todi, S. V., Tsou, W. L. (2024). Progressive degeneration in a new Drosophila model of spinocerebellar ataxia type 7. Sci Rep, 14(1):14332 PubMed ID: 38906973
Summary:
Spinocerebellar ataxia type 7 (SCA7) is a progressive neurodegenerative disorder resulting from abnormal expansion of an uninterrupted polyglutamine (polyQ) repeat in its disease protein, ataxin-7 (ATXN7). ATXN7 is part of Spt-Ada-Gcn5 acetyltransferase (SAGA), an evolutionarily conserved transcriptional coactivation complex with critical roles in chromatin remodeling, cell signaling, neurodifferentiation, mitochondrial health and autophagy. SCA7 is dominantly inherited and characterized by genetic anticipation and high repeat-length instability. Patients with SCA7 experience progressive ataxia, atrophy, spasticity, and blindness. There is currently no cure for SCA7, and therapies are aimed at alleviating symptoms to increase quality of life. This studhy reports novel Drosophila lines of SCA7 with polyQ repeats in wild-type and human disease patient range. ATXN7 expression has age- and polyQ repeat length-dependent reduction in fruit fly survival and retinal instability, concomitant with increased ATXN7 protein aggregation. These new lines will provide important insight on disease progression that can be used in the future to identify therapeutic targets for SCA7 patients.

Sevegnani, M., Lama, A., Girardi, F., Hess, M. W., Castelo, M. P., Pichler, I., Biressi, S., Piccoli, G. (2024). Parkin R274W mutation affects muscle and mitochondrial physiology. Biochimica et biophysica acta Molecular basis of disease. 1870(7):167302 PubMed ID: 38878834
Summary:
Recessive mutations in the Parkin gene (PRKN) are the most common cause of young-onset inherited parkinsonism. Parkin is a multifunctional E3 ubiquitin ligase that plays a variety of roles in the cell including the degradation of proteins and the maintenance of mitochondrial homeostasis, integrity, and biogenesis. In 2001, the R275W mutation in the PRKN gene was identified in two unrelated families with a multigenerational history of postural tremor, dystonia and parkinsonism. Drosophila models of Parkin R275W showed selective and progressive degeneration of dopaminergic neuronal clusters, mitochondrial abnormalities, and prominent climbing defects. In the Prkn mouse orthologue, the amino acid R274 corresponds to human R275. Here we described an age-related motor impairment and a muscle phenotype in R274W +/+ mice. In vitro, Parkin R274W mutation correlates with abnormal myoblast differentiation, mitochondrial defects, and alteration in mitochondrial mRNA and protein levels. These data suggest that the Parkin R274W mutation may impact mitochondrial physiology and eventually myoblast proliferation and differentiation.

Tuesday, April 1st - Signalling

Lee, G. G., Peterson, A. J., Kim, M. J., O'Connor, M. B., Park, J. H. (2024). Multiple isoforms of the Activin-like receptor baboon differentially regulate proliferation and conversion behaviors of neuroblasts and neuroepithelial cells in the Drosophila larval brain. PLoS One, 19(6):e0305696 PubMed ID: 38913612
Summary:
In Drosophila coordinated proliferation of two neural stem cells, neuroblasts (NB) and neuroepithelial (NE) cells, is pivotal for proper larval brain growth that ultimately determines the final size and performance of an adult brain. The larval brain growth displays two phases based on behaviors of NB and NEs: the first one in early larval stages, influenced by nutritional status and the second one in the last larval stage, promoted by ecdysone signaling after critical weight checkpoint. Mutations of the baboon (babo) gene that produces three isoforms (BaboA-C), all acting as type-I receptors of Activin-type transforming growth factor β (TGF-β) signaling, cause a small brain phenotype due to severely reduced proliferation of the neural stem cells. This study show that loss of babo function severely affects proliferation of NBs and NEs as well as conversion of NEs from both phases. By analyzing babo-null and newly generated isoform-specific mutants by CRISPR mutagenesis as well as isoform-specific RNAi knockdowns in a cell- and stage-specific manner, the data support differential contributions of the isoforms for these cellular events with BaboA playing the major role. Stage-specific expression of EcR-B1 in the brain is also regulated primarily by BaboA along with function of the other isoforms. Blocking EcR function in both neural stem cells results in a small brain phenotype that is more severe than baboA-knockdown alone. In summary, this study proposes that the Babo-mediated signaling promotes proper behaviors of the neural stem cells in both phases and achieves this by acting upstream of EcR-B1 expression in the second phase.

Wodrich, A. P. K., Harris, B. T., Giniger, E. (2024). Changes in mitochondrial distribution occur at the axon initial segment in association with neurodegeneration in Drosophila. Biol Open, 13(7) PubMed ID: 38912559
Summary:
Changes in mitochondrial distribution are a feature of numerous age-related neurodegenerative diseases. In Drosophila, reducing the activity of Cdk5 causes a neurodegenerative phenotype and is known to affect several mitochondrial properties. Therefore, this study investigated whether alterations of mitochondrial distribution are involved in Cdk5-associated neurodegeneration. Reducing Cdk5 activity did not alter the balance of mitochondrial localization to the somatodendritic versus axonal neuronal compartments of the mushroom body, the learning and memory center of the Drosophila brain. Changes in mitochondrial distribution were observed at the axon initial segment (AIS), a neuronal compartment located in the proximal axon involved in neuronal polarization and action potential initiation. Specifically, its was observed that mitochondria are partially excluded from the AIS in wild-type neurons, but that this exclusion is lost upon reduction of Cdk5 activity, concomitant with the shrinkage of the AIS domain that is known to occur in this condition. This mitochondrial redistribution into the AIS is not likely due to the shortening of the AIS domain itself but rather due to altered Cdk5 activity. Furthermore, mitochondrial redistribution into the AIS is unlikely to be an early driver of neurodegeneration in the context of reduced Cdk5 activity.

Sharma, V., Sachan, N., Sarkar, B., Mutsuddi, M., Mukherjee, A. (2024). E3 ubiquitin ligase Deltex facilitates the expansion of Wingless gradient and antagonizes Wingless signaling through a conserved mechanism of transcriptional effector Armadillo/β-catenin degradation. Elife, 12 PubMed ID: 38900140
Summary:
The Wnt/Wg pathway controls myriads of biological phenomena throughout the development and adult life of all organisms across the phyla. Thus, an aberrant Wnt signaling is associated with a wide range of pathologies in humans. Tight regulation of Wnt/Wg signaling is required to maintain proper cellular homeostasis. This study reports a novel role of E3 ubiquitin ligase Deltex in Wg signaling regulation. Drosophila dx genetically interacts with wg and its pathway components. Furthermore, Dx LOF results in a reduced spreading of Wg while its over-expression expands the diffusion gradient of the morphogen. This change is attributed to change in Wg gradient to the endocytosis of Wg through Dx which directly affects the short- and long-range Wg targets. The role of Dx in regulating Wg effector Armadillo was demonstrated where Dx down-regulates Arm through proteasomal degradation. This study also showed the conservation of Dx function in the mammalian system where DTX1 is shown to bind with β-catenin and facilitates its proteolytic degradation, spotlighting a novel step that potentially modulates Wnt/Wg signaling cascade.

Singh, K., Das, S., Sutradhar, S., Howard, J., Ray, K. (2024). Insulin signaling accelerates the anterograde movement of Rab4 vesicles in axons through Klp98A/KIF16B recruitment via Vps34-PI3Kinase. bioRxiv, PubMed ID: 38895253
Summary:
Rab4 GTPase organizes endosomal sorting essential for maintaining the balance between recycling and degradative pathways. Rab4 localizes to many cargos whose transport in neurons is critical for regulating neurotransmission and neuronal health. Furthermore, elevated Rab4 levels in the CNS are associated with synaptic atrophy and neurodegeneration in Drosophila and humans, respectively. However, how the transport of Rab4-associated vesicles is regulated in neurons remains unknown. Using in vivo time-lapse imaging of Drosophila larvae, this study showd that activation of insulin signaling via Dilp2 and dInR increases the anterograde velocity, run length, and flux of Rab4 vesicles in the axons. Molecularly, activation of neuronal insulin signaling further activates Vps34, elevates the levels of PI(3)P on Rab4-associated vesicles, recruits Klp98A (a PI(3)P-binding kinesin-3 motor) and activates their anterograde transport. Together, these observations delineate the role of insulin signaling in regulating axonal transport and synaptic homeostasis.

Malinauskas, T., Moore, G., Rudolf, A. F., Eggington, H., Belnoue-Davis, H. L., El Omari, K., Griffiths, S. C., Woolley, R. E., Duman, R., Wagner, A., Leedham, S. J., Baldock, C., Ashe, H. L., Siebold, C. (2024). Molecular mechanism of BMP signal control by Twisted gastrulation. Nat Commun, 15(1):4976 PubMed ID: 38862520
Summary:
Twisted gastrulation (TWSG1) is an evolutionarily conserved secreted glycoprotein which controls signaling by Bone Morphogenetic Proteins (BMPs). TWSG1 binds BMPs and their antagonist Chordin to control BMP signaling during embryonic development, kidney regeneration and cancer. This study reports crystal structures of TWSG1 alone and in complex with a BMP ligand, Growth Differentiation Factor 5. TWSG1 is composed of two distinct, disulfide-rich domains. The TWSG1 N-terminal domain occupies the BMP type 1 receptor binding site on BMPs, whereas the C-terminal domain binds to a Chordin family member. TWSG1 inhibits BMP function in cellular signaling assays and mouse colon organoids. This inhibitory function is abolished in a TWSG1 mutant that cannot bind BMPs. The same mutation in the Drosophila TWSG1 ortholog Tsg fails to mediate BMP gradient formation required for dorsal-ventral axis patterning of the early embryo. These studies reveal the evolutionarily conserved mechanism of BMP signaling inhibition by TWSG1.

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