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Current papers in developmental biology and gene function
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| ARCHIVE | Monday, September 30th - Gonads |
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What's hot today
October 2024 September 2024 August 2024 July 2024 June 2024 May 2024 April 2024 March 2024 February 2024 January 2024 December 2023 November 2023 October 2023 September 2023 August 2023 July 2023 June 2023 May 2023 April 2023 March 2023 February 2023 January 2023 December 2022 December 2021 December 2020 December 2019 December 2018 | Barton, L. J., Sanny, J., Packard Dawson, E., Nouzova, M., Noriega, F. G., Stadtfeld, M., Lehmann, R. (2024). Juvenile hormones direct primordial germ cell migration to the embryonic gonad. Curr Biol, PubMed ID: 38215744
Summary: Germ cells are essential to sexual reproduction. Across the animal kingdom, extracellular signaling isoprenoids, such as retinoic acids (RAs) in vertebrates and juvenile hormones (JHs) in invertebrates, facilitate multiple processes in reproduction. This study investigated the role of these potent signaling molecules in embryonic germ cell development, using JHs in Drosophila melanogaster as a model system. In contrast to their established endocrine roles during larval and adult germline development, it was found that JH signaling acts locally during embryonic development. Using an in vivo biosensor, active JH signaling was observed first within and near primordial germ cells (PGCs) as they migrate to the developing gonad. Through in vivo and in vitro assays, it was determined that JHs are both necessary and sufficient for PGC migration. Analysis into the mechanisms of this newly uncovered paracrine JH function revealed that PGC migration was compromised when JHs were decreased or increased, suggesting that specific titers or spatiotemporal JH dynamics are required for robust PGC colonization of the gonad. Compromised PGC migration can impair fertility and cause germ cell tumors in many species, including humans. In mammals, retinoids have many roles in development and reproduction. Like JHs in Drosophila, RA was found to be sufficient to impact mouse PGC migration in vitro. Together, this study reveals a previously unanticipated role of isoprenoids as local effectors of pre-gonadal PGC development and suggests a broadly shared mechanism in PGC migration. | Grmai, L., Jimenez, E., Baxter, E., Van Doren, M. (2023). Steroid signaling controls sex-specific development in an invertebrate. bioRxiv, PubMed ID: 38187640
Summary: In vertebrate sexual development, two important steroid hormones - testosterone and estrogen - regulate the sex-specific development of many tissues. In contrast, invertebrates utilize a single steroid hormone, ecdysone, to regulate developmental timing in both sexes. This study shows that in the fruit fly Drosophila melanogaster, sex-specific ecdysone activity controls important aspects of gonad sexual dimorphism. Rather than being regulated at the level of hormone production, hormone activity is regulated cell-autonomously through sex-specific hormone reception. Ecdysone receptor (EcR) was found to regulate downstream of the sex determination factor Doublesex (Dsx), the founding member of the Dsx/Mab3 Related Transcription Factor (DMRT) family that regulates gonad development in all animals. EcR is restricted to the developing ovary and repressed in the testis at a time when ecdysone initiates ovary morphogenesis. EcR activity drives ovary development and antagonizes development of the testis stem cell niche. Interestingly, de-repression of the ecdysone response in the testis led to rapid feminization, which is known to cause infertility. This work demonstrates that invertebrates can also use steroid hormone signaling to control sex-specific development. Further, it may help explain recent work showing that vertebrate sexual development is surprisingly cell-autonomous. For example, in birds that have a mixture of cells with male and female genotypes, the male cells develop as male and the female cells develop as female despite exposure to the same circulating hormones. Sex-specific regulation of steroid hormone response in vertebrates may well underly such cellular sexual fate choices. |
| Liu, X., Li, X., Wang, Z. (2024). The spatiotemporal pattern of glypican coordinates primordial germ cell differentiation with ovary development. iScience, 27(1):108710 PubMed ID: 38205252
Summary: The establishment, proliferation, and differentiation of stem cells are coordinated with organ development and regulated by the signals in the microenvironment. Prior to gonad formation, how primordial germ cells (PGC) differentiate spatiotemporally to coordinate with gonadogenesis is unclear. In adult ovary, Drosophila extracellular glypican Dally in germline stem cell (GSC) niche promotes BMP signaling to inhibit germline differentiation. This study investigated the relation between the fate of PGC and the spatiotemporal pattern of glypican during ovary development. Dally in ovarian soma was shown to assisted BMP signaling to prevent PGC from precocious differentiation. Dally's presence raises the "hurdle" for ecdysone peaks to eventually remove the transcription factor Kr and de-repress pro-differentiation factor, temporally postponing PGC differentiation until GSC niche establishment. The spatiotemporal glypican in somatic matrix assists PGC to integrate the ovarian local BMP and organismal steroid signals that coordinate PGC's program with organ/body development to maximize reproductive potential. | Sadanandappa, M. K., Bosco, G. (2024). Parasitoid cues modulate Drosophila germline development and stem cell proliferation.Cell Rep, 43(1):113657 PubMed ID: 38175752
Summary: Environmental factors influence an organism's reproductive ability by regulating germline development and physiology. While the reproductive adaptations in response to extrinsic stress cues offer fitness and survival advantages to individuals, the mechanistic understanding of these modifications remains unclear. This study found that parasitoid wasps' stress signaling regulates Drosophila melanogaster oogenesis. Fruit flies dwelling in the wasp-infested area were found to elevate their fecundity, and the observed reproductive response is specific to Pachycrepoideus sp., a pupal parasitoid wasp. Pachycrepoideus-specific olfactory and visual cues recruit the signaling pathways that promote germline stem cell proliferation and accelerate follicle development, increasing egg production in Drosophila females. Downregulation of signaling engaged in oocyte development by shifting flies to a non-wasp-infested environment increases apoptosis of the developing follicles. Thus, this study establishes host germline responsiveness to parasitoid-specific signals and supports a predator strategy to increase hosts for infection. |
| Weng, R. Y., Zhang, L., Liu, J. L. (2024). Connecting Hippo Pathway and Cytoophidia in Drosophila Posterior Follicle Cells. Int J Mol Sci, 25(3) PubMed ID: 38338731
Summary: CTP synthase (CTPS), the rate-limiting enzyme in the de novo synthesis of CTP, assembles into a filamentous structure termed the cytoophidium. The Hippo pathway regulates cell proliferation and apoptosis. The relationship of the nucleotide metabolism with the Hippo pathway is little known. This study examined the impact of the Hippo pathway on the cytoophidium in Drosophila melanogaster posterior follicle cells (PFCs). Inactivation of the Hippo pathway was found to correlates with reduced cytoophidium length and number within PFCs. During the overexpression of CTPS, the presence of Hippo mutations also reduces the length of cytoophidia in PFCs. In addition, it was observed that knocking down CTPS mitigates hpo (Hippo)-associated over-proliferation. In summary, these results suggest that there is a connection between the Hippo pathway and the nucleotide biosynthesis enzyme CTPS in PFCs. | Lepesant, J. A., Roland-Gosselin, F., Guillemet, C., Bernard, F., Guichet, A. (2024). The Importance of the Position of the Nucleus in Drosophila Oocyte Development. Cells, 13(2) PubMed ID: 38275826
Summary: Oogenesis is a developmental process leading to the formation of an oocyte, a haploid gamete, which upon fertilisation and sperm entry allows the male and the female pronuclei to fuse and give rise to a zygote. In addition to forming a haploid gamete, oogenesis builds up a store of proteins, mRNAs, and organelles in the oocyte needed for the development of the future embryo. In several species, such as Drosophila, the polarity axes determinants of the future embryo must be asymmetrically distributed prior to fertilisation. In the Drosophila oocyte, the correct positioning of the nucleus is essential for establishing the dorsoventral polarity axis of the future embryo and allowing the meiotic spindles to be positioned in close vicinity to the unique sperm entry point into the oocyte. |
Thursday, September 26th - Adult Development |
| Tran, N. V., Montanari, M. P., Gui, J., Lubenets, D., Fischbach, L. L., Antson, H., Huang, Y., Brutus, E., Okada, Y., Ishimoto, Y., Tonissoo, T., Shimmi, O. (2024). Programmed disassembly of a microtubule-based membrane protrusion network coordinates 3D epithelial morphogenesis in Drosophila. The EMBO journal, 43(4):568-594 PubMed ID: 38263333
Summary: Comprehensive analysis of cellular dynamics during the process of morphogenesis is fundamental to understanding the principles of animal development. Despite recent advancements in light microscopy, how successive cell shape changes lead to complex three-dimensional tissue morphogenesis is still largely unresolved. Using in vivo live imaging of Drosophila wing development, Unique cellular structures comprising a microtubule-based membrane protrusion network was studied. This network, which is name in this study the Interplanar Amida Network (IPAN), links the two wing epithelium leaflets. Initially, the IPAN sustains cell-cell contacts between the two layers of the wing epithelium through basal protrusions. Subsequent disassembly of the IPAN involves loss of these contacts, with concomitant degeneration of aligned microtubules. These processes are both autonomously and non-autonomously required for mitosis, leading to coordinated tissue proliferation between two wing epithelia. These findings further reveal that a microtubule organization switch from non-centrosomal to centrosomal microtubule-organizing centers (MTOCs) at the G2/M transition leads to disassembly of non-centrosomal microtubule-derived IPAN protrusions. These findings exemplify how cell shape change-mediated loss of inter-tissue contacts results in 3D tissue morphogenesis. | Navarro, T., Iannini, A., Neto, M., Campoy-Lopez, A., Munoz-Garcia, J., Pereira, P. S., Ares, S., Casares, F. (2024).. Feedback control of organ size precision is mediated by BMP2-regulated apoptosis in the Drosophila eye. PLoS Biol, 22(1):e3002450 PubMed ID: 38289899
Summary: Biological processes are intrinsically noisy, and yet, the result of development-like the species-specific size and shape of organs-is usually remarkably precise. This precision suggests the existence of mechanisms of feedback control that ensure that deviations from a target size are minimized. Still, there is very limited understanding of how these mechanisms operate. This study investigated the problem of organ size precision using the Drosophila eye. The size of the adult eye depends on the rates at which eye progenitor cells grow and differentiate. It was first found that the progenitor net growth rate results from the balance between their proliferation and apoptosis, with this latter contributing to determining both final eye size and its variability. In turn, apoptosis of progenitor cells is hampered by Dpp, a BMP2/4 signaling molecule transiently produced by early differentiating retinal cells. Genetic and computational experiments show how the status of retinal differentiation is communicated to progenitors through the differentiation-dependent production of Dpp, which, by adjusting the rate of apoptosis, exerts a feedback control over the net growth of progenitors to reduce final eye size variability. |
| George, L. F., Follmer, M. L., Fontenoy, E., Moran, H. R., Brown, J. R., Ozekin, Y. H., Bates, E. A. (2023). Endoplasmic Reticulum Calcium Mediates Drosophila Wing Development. Bioelectricity, 5(4):290-306 PubMed ID: 38143873
Summary: The temporal dynamics of morphogen presentation impacts transcriptional responses and tissue patterning. However, the mechanisms controlling morphogen release are far from clear. This study found that inwardly rectifying potassium (Irk) channels regulate endogenous transient increases in intracellular calcium and bone morphogenetic protein (BMP/Dpp) release for Drosophila wing development. Inhibition of Irk channels reduces BMP/Dppsignaling, and ultimately disrupts wing morphology. Ion channels impact development of several tissues and organisms in which BMP signaling is essential. In neurons and pancreatic beta cells, Irk channels modulate membrane potential to affect intracellular Ca(++) to control secretion of neurotransmitters and insulin. Based on Irk activity in neurons, it is hypothesized that electrical activity controls endoplasmic reticulum (ER) Ca(++) release into the cytoplasm to regulate the release of BMP. | Rosa-Birriel, C., Malin, J., Hatini, V. (2024). Medioapical contractile pulses coordinated between cells regulate Drosophila eye morphogenesis. J Cell Biol, 223(2) PubMed ID: 38126997
Summary: Lattice cells (LCs) in the developing Drosophila retina change shape before attaining final form. Previously, it has been shown that repeated contraction and expansion of apical cell contacts affect these dynamics. Another factor is described, the assembly of a Rho1-dependent medioapical actomyosin ring formed by nodes linked by filaments that contract the apical cell area. Cell area contraction alternates with relaxation, generating pulsatile changes in cell area that exert force on neighboring LCs. Moreover, Rho1 signaling is sensitive to mechanical changes, becoming active when tension decreases and cells expand, while the negative regulator RhoGAP71E accumulates when tension increases and cells contract. This results in cycles of cell area contraction and relaxation that are reciprocally synchronized between adjacent LCs. Thus, mechanically sensitive Rho1 signaling controls pulsatile medioapical actomyosin contraction and coordinates cell behavior across the epithelium. Disrupting the kinetics of pulsing can lead to developmental errors, suggesting this process controls cell shape and tissue integrity during epithelial morphogenesis of the retina. |
| Contreras, F. V., Auger, G. M., Muller, L., Richter, V., Huetteroth, W., Seufert, F., Hildebrand, P. W., Scholz, N., Thum, A. S., Ljaschenko, D., Blanco-Redondo, B., Langenhan, T. (2024). The adhesion G-protein-coupled receptor mayo/CG11318 controls midgut development in Drosophila. Cell Rep, 43(1):113640 PubMed ID: 38180839
Summary: Adhesion G-protein-coupled receptors (aGPCRs) form a large family of cell surface molecules with versatile tasks in organ development. Many aGPCRs still await their functional and pharmacological deorphanization. This study characterized the orphan aGPCR mayoKO mutants can be restored by pharmacological inhibition of potassium channels. Intriguingly, hyperkalemia and tachycardia are caused non-cell autonomously through mayo-dependent control of enterocyte proliferation in the larval midgut, which is the primary function of this aGPCR. These findings characterize the ancestral aGPCR Mayo as a homeostatic regulator of gut development. | Banerjee, S. J., Curtiss, J. (2024). Dachshund and C-terminal Binding Protein bind directly during Drosophila eye development. microPublication biology, 2024 PubMed ID: 38528987
Summary: The transcription factor Dachshund (Dac) and the transcriptional co-regulator C-terminal Binding Protein (CtBP) were identified as the retinal determination factors during Drosophila eye development . A previous study established that Dac and CtBP interact genetically during eye development. Co-immunoprecipitation assays suggested that both molecules interact in the Drosophila larval eye-antennal disc. This study shows that Dac and CtBP bind each other directly, as determined by GST pull-down assays. Thus, these results demonstrate the molecular mechanism of Dac and CtBP interaction and suggest the direct binding of these two transcription regulators in the cells of the eye disc promotes the Drosophila eye specification. |
Thursday, September 19th - Adult Neural Development, Structure and Function |
| Schneps, C. M., Dunleavy, R., Crane, B. R. (2024). Dissecting the Interaction between Cryptochrome and Timeless Reveals Underpinnings of Light-Dependent Recognition. Biochemistry, PubMed ID: 38294880
Summary: Circadian rhythms are determined by cell-autonomous transcription-translation feedback loops that entrain to environmental stimuli. In the model circadian clock of Drosophila melanogaster, the clock is set by the light-induced degradation of the core oscillator protein Timeless (TIM) by the principal light-sensor cryptochrome (CRY). The cryo-EM structure of CRY bound to TIM revealed that within the extensive CRY:TIM interface, the TIM N-terminus binds into the CRY FAD pocket, in which FAD and the associated phosphate-binding loop (PBL) undergo substantial rearrangement. The TIM N-terminus involved in CRY binding varies in isoforms that facilitate the adaptation of flies to different light environments. This study demonstrates, through peptide binding assays and pulsed-dipolar electron spin resonance (ESR) spectroscopy, that the TIM N-terminal peptide alone exhibits light-dependent binding to CRY and that the affinity of the interaction depends on the initiating methionine residue. Extensions to the TIM N-terminus that mimic less light-sensitive variants have substantially reduced interactions with CRY. Substitutions of CRY residues that couple to the flavin rearrangement in the CRY:TIM complex have dramatic effects on CRY light activation. CRY residues Arg237 on α8, Asn253, and Gln254 on the PBL are critical for the release of the CRY autoinhibitory C-terminal tail (CTT) and subsequent TIM binding. These key light-responsive elements of CRY are well conserved throughout Type I cryptochromes of invertebrates but not by cryptochromes of chordates and plants, which likely utilize a distinct light-activation mechanism. | Pettersson, J. H., Cattaneo, A. M. (2023). Heterologous investigation of metabotropic and ionotropic odorant receptors in ab3A neurons of Drosophila melanogaster. Front Mol Biosci, 10:1275901 PubMed ID: 38344364
Summary: In insects, antennal ionotropic receptors (IRs) and odorant receptors (ORs) are among the main sensors of olfactory cues. To functionally characterize the subunits from these receptors, the use of ab3A neurons from transgenic Drosophila melanogaster represented one of the most powerful tools, allowing the identification of ligands (deorphanization) and decrypting their pharmacological properties. However, further investigation is needed to shed light on possible metabotropic functionalities behind insect olfactory receptors and test potentials from the up-to-now-used empty neuronal systems to express subunits belonging to variegate receptor classes. This project adopted the most updated system of Drosophila ab3A empty neurons to test various olfactory receptors, ranging from human ORs working as metabotropic G-protein coupled receptors to insect ionotropic IRs and ORs. Testing transgenic Drosophila expressing human ORs into ab3A neurons by single sensillum recording did not result in an OR response to ligands, but it rather re-established neuronal spiking from the empty neurons. When transgenic D. melanogaster expressed ionotropic IRs and ORs, both heterologous and cis-expressed IRs were non-functional, but the Drosophila suzukii OR19A1 subunit responded to a wide asset of ligands, distinguishing phasic or tonic compound-dependent effects. Despite the use of Drosophila ab3A neurons to test the activation of some metabotropic and ionotropic receptor subunits resulted non-functional, this study deorphanized a key OR of D. suzukii demonstrating its binding to alcohols, ketones, terpenes, and esters. |
| Simon, F., Holguera, I., Chen, Y. C., Malin, J., Valentino, P., Erclik, T., Desplan, C. (2024). High-throughput identification of the spatial origins of Drosophila optic lobe neurons using single-cell mRNA-sequencing. bioRxiv, PubMed ID: 38370610
Summary: The medulla is the largest neuropil of the Drosophila optic lobe. It contains about 100 neuronal types that have been comprehensively characterized morphologically and molecularly. These neuronal types are specified from a larval neuroepithelium called the Outer Proliferation Center (OPC) via the integration of temporal, spatial, and Notch-driven mechanisms. Although the temporal windows of origin of all medulla neurons, as well as their Notch status, have been e recently characterized their spatial origins remained unknown. This study isolated cells from different OPC spatial domains and performed single-cell mRNA-sequencing to identify the neuronal types produced in these domains. This allowed characterization in a high-throughput manner the spatial origins of all medulla neurons and to identify two new spatial subdivisions of the OPC. Moreover, this work shows that the most abundant neuronal types are produced from epithelial domains of different sizes despite being present in a similar number of copies. Combined with previously published scRNA-seq developmental atlas of the optic lobe, this work opens the door for further studies on how specification factor expression in progenitors impacts gene expression in developing and adult neurons. | Price, M. S., Moore, T. I., Venkatachalam, K. (2024). Intracellular Lactate Dynamics Reveal the Metabolic Diversity of Drosophila Glutamatergic Neurons. bioRxiv, PubMed ID: 38464270
Summary: Lactate, an intermediary between glycolysis and mitochondrial oxidative phosphorylation, reflects the metabolic state of neurons. This study utilized a genetically-encoded lactate FRET biosensor to uncover subpopulations of distinct metabolic states among Drosophila glutamatergic neurons. Neurons within specific subpopulations exhibited correlated lactate flux patterns that stemmed from inherent cellular properties rather than neuronal interconnectivity. Further, individual neurons exhibited consistent patterns of lactate flux over time such that stimulus-evoked changes in lactate were correlated with pre-treatment fluctuations. Leveraging these temporal autocorrelations, deep-learning models accurately predicted post-stimulus responses from pre-stimulus fluctuations. These findings point to the existence of distinct neuronal subpopulations, each characterized by unique lactate dynamics, and raise the possibility that neurons with correlated >metabolic activities might synchronize across different neural circuits. Such synchronization, rooted in neuronal metabolic states, could influence information processing in the brain. |
| Kim, D. H., Jang, Y. H., Yun, M., Lee, K. M., Kim, Y. J. (2024). Long-term neuropeptide modulation of female sexual drive via the TRP channel in Drosophila melanogaster. Proc Natl Acad Sci U S A, 121(10):e2310841121 PubMed ID: 38412134
Summary: Connectomics research has made it more feasible to explore how neural circuits can generate multiple outputs. Female sexual drive provides a good model for understanding reversible, long-term functional changes in motivational circuits. After emerging, female flies avoid male courtship, but they become sexually receptive over 2 d. Mating causes females to reject further mating for several days. This study reports that pC1 neurons, which process male courtship and regulate copulation behavior, exhibit increased CREB (cAMP response element binding protein) activity during sexual maturation and decreased CREB activity after mating. This increased CREB activity requires the neuropeptide Dh44 (Diuretic hormone 44) and its receptors. A subset of the pC1 neurons secretes Dh44, which stimulates CREB activity and increases expression of the TRP channel Pyrexia (Pyx) in more pC1 neurons. This, in turn, increases pC1 excitability and sexual drive. Mating suppresses pyx expression and pC1 excitability. Dh44 is orthologous to the conserved corticotrophin-releasing hormone family, suggesting similar roles in other species. | Ye, D., Walsh, J. T., Junker, I. P., Ding, Y. (2024). Changes in the cellular makeup of motor patterning circuits drive courtship song evolution in Drosophila. bioRxiv, PubMed ID: 38328135
Summary: How evolutionary changes in genes and neurons encode species variation in complex motor behaviors are largely unknown. This study developed genetic tools that permit a neural circuit comparison between the model species Drosophila melanogaster and the closely-related species D. yakuba, who has undergone a lineage-specific loss of sine song, one of the two major types of male courtship song in Drosophila. Neuroanatomical comparison of song patterning neurons called TN1 across the phylogeny demonstrates a link between the loss of sine song and a reduction both in the number of TN1 neurons and the neurites serving the sine circuit connectivity. Optogenetic activation confirms that TN1 neurons in D. yakuba have lost the ability to drive sine song, while maintaining the ability to drive the singing wing posture. Single-cell transcriptomic comparison shows that D. yakuba specifically lacks a cell type corresponding to TN1A neurons, the TN1 subtype that is essential for sine song. Genetic and developmental manipulation reveals a functional divergence of the sex determination gene doublesex in D. yakuba to reduce TN1 number by promoting apoptosis. This work illustrates the contribution of motor patterning circuits and cell type changes in behavioral evolution, and uncovers the evolutionary lability of sex determination genes to reconfigure the cellular makeup of neural circuits. |
Wednesday September 18th - Disease Models |
| Martinez, A., Sanchez-Martinez, A., Pickering, J. T., Twyning, M. J., Terriente-Felix, A., Chen, P. L., Chen, C. H., Whitworth, A. J. (2024). Mitochondrial CISD1/Cisd accumulation blocks mitophagy and genetic or pharmacological inhibition rescues neurodegenerative phenotypes in Pink1/parkin models. Molecular neurodegeneration, 19(1):12 PubMed ID: 38273330
Summary: Mitochondrial dysfunction and toxic protein aggregates have been shown to be key features in the pathogenesis of neurodegenerative diseases, such as Parkinson's disease (PD). Functional analysis of genes linked to PD have revealed that the E3 ligase Parkin and the mitochondrial kinase PINK1 are important factors for mitochondrial quality control. PINK1 phosphorylates and activates Parkin, which in turn ubiquitinates mitochondrial proteins priming them and the mitochondrion itself for degradation. However, it is unclear whether dysregulated mitochondrial degradation or the toxic build-up of certain Parkin ubiquitin substrates is the driving pathophysiological mechanism leading to PD. The iron-sulphur cluster containing proteins CISD1 and CISD2 (see DSID) have been identified as major targets of Parkin in various proteomic studies. This study employed in vivo Drosophila and human cell culture models to study the role of CISD proteins in cell and tissue viability as well as aged-related neurodegeneration, specifically analysing aspects of mitophagy and autophagy using orthogonal assays. The Drosophila homolog Cisd was shown to accumulate in Pink1 and parkin mutant flies, as well as during ageing. It was observed that build-up of Cisd is particularly toxic in neurons, resulting in mitochondrial defects and Ser65-phospho-Ubiquitin accumulation. Age-related increase of Cisd blocks mitophagy and impairs autophagy flux. Importantly, reduction of Cisd levels upregulates mitophagy in vitro and in vivo, and ameliorates pathological phenotypes in locomotion, lifespan and neurodegeneration in Pink1/parkin mutant flies. In addition, pharmacological inhibition of CISD1/2 by rosiglitazone and NL-1 was shown to induce mitophagy in human cells and ameliorate the defective phenotypes of Pink1/parkin mutants. Altogether, these studies indicate that Cisd accumulation during ageing and in Pink1/parkin mutants is a key driver of pathology by blocking mitophagy, and genetically and pharmacologically inhibiting CISD proteins may offer a potential target for therapeutic intervention. | Schultheis, N., Connell, A., Kapral, A., Becker, R. J., Mueller, R., Shah, S., O'Donnell, M., Roseman, M., Wang, W., Yin, F., Weiss, R., Selleck, S. B. (2024). Heparan sulfate modified proteins affect cellular processes central to neurodegeneration and modulate presenilin function.. bioRxiv, PubMed ID: 38328107
Summary: Mutations in presenilin-1 (PSEN1) are the most common cause of familial, early-onset Alzheimer's disease (AD), typically producing cognitive deficits in the fourth decade. A variant of APOE, APOE3 Christchurch (APOE3ch) , was found associated with protection from both cognitive decline and Tau accumulation in a 70-year-old bearing the disease-causing PSEN1-E280A mutation. The amino acid change in ApoE3ch is within the heparan sulfate (HS) binding domain of APOE, and purified APOEch showed dramatically reduced affinity for heparin, a highly sulfated form of HS. The physiological significance of ApoE3ch is supported by studies of a mouse bearing a knock-in of this human variant and its effects on microglia reactivity and Aβ-induced Tau deposition. These studies examined the function of heparan sulfate-modified proteoglycans (HSPGs) in cellular and molecular pathways affecting AD-related cell pathology in human cell lines and mouse astrocytes. The mechanisms of HSPG influences on presenilin- dependent cell loss and pathology were evaluated in Drosophila using knockdown of the presenilin homolog, Psn , together with partial loss of function of sulfateless (sfl) , a homolog of NDST1 , a gene specifically affecting HS sulfation. HSPG modulation of autophagy, mitochondrial function, and lipid metabolism were shown to be conserved in cultured human cell lines, Drosophila, and mouse astrocytes. RNAi of Ndst1 reduced intracellular lipid levels in wild-type mouse astrocytes or those expressing humanized variants of APOE, APOE3 , and APOE4 . RNA-sequence analysis of human cells deficient in HS synthesis demonstrated effects on the transcriptome governing lipid metabolism, autophagy, and mitochondrial biogenesis and showed significant enrichment in AD susceptibility genes identified by GWAS. Neuron-directed knockdown of Psn in Drosophila produced cell loss in the brain and behavioral phenotypes, both suppressed by simultaneous reductions in sfl mRNA levels. Abnormalities in mitochondria, liposome morphology, and autophagosome-derived structures in animals with Psn knockdown were also rescued by simultaneous reduction of sfl. sfl knockdown reversed Psn- dependent transcript changes in genes affecting lipid transport, metabolism, and monocarboxylate carriers. These findings support the direct involvement of HSPGs in AD pathogenesis. |
| Le, M. U. T., Park, J. H., Son, J. G., Shon, H. K., Joh, S., Chung, C. G., Cho, J. H., Pirkl, A., Lee, S. B., Lee, T. G. (2024). Monitoring lipid alterations in Drosophila heads in an amyotrophic lateral sclerosis model with time-of-flight secondary ion mass spectrometry. The Analyst, 149(3):846-858 PubMed ID: 38167886
Summary: Lipid alterations in the brain are well-documented in disease and aging, but understanding of their pathogenic implications remains incomplete. Recent technological advances in assessing lipid profiles have enabled intricate examination of the spatiotemporal variations in lipid compositions within the complex brain characterized by diverse cell types and intricate neural networks. This study coupled time-of-flight secondary ion mass spectrometry (ToF-SIMS) to an amyotrophic lateral sclerosis (ALS) Drosophila model, for the first time, to elucidate changes in the lipid landscape and investigate their potential role in the disease process, serving as a methodological and analytical complement to a prior approach that utilized matrix-assisted laser desorption/ionization mass spectrometry. The expansion of G(4)C(2) repeats in the C9orf72 gene is the most prevalent genetic factor in ALS. The findings indicate that expressing these repeats in fly brains elevates the levels of fatty acids, diacylglycerols, and ceramides during the early stages (day 5) of disease progression, preceding motor dysfunction. Using RNAi-based genetic screening targeting lipid regulators, it esd found that reducing fatty acid transport protein 1 (FATP1) and Acyl-CoA-binding protein (ACBP) alleviates the retinal degeneration caused by G(4)C(2) repeat expression and also markedly restores the G(4)C(2)-dependent alterations in lipid profiles. Significantly, the expression of FATP1 and ACBP is upregulated in G(4)C(2)-expressing flies, suggesting their contribution to lipid dysregulation. Collectively, novel use of ToF-SIMS with the ALS Drosophila model, alongside methodological and analytical improvements, successfully identifies crucial lipids and related genetic factors in ALS pathogenesis. | Davis, G. H., Zaya, A., Pearce, M. M. P. (2024). Impairment of the glial phagolysosomal system drives prion-like propagation in a Drosophila model of Huntington's disease. JbioRxiv, PubMed ID: 38370619
Summary: Protein misfolding, aggregation, and spread through the brain are primary drivers of neurodegenerative diseases pathogenesis. Phagocytic glia are responsible for regulating the load of pathogenic protein aggregates in the brain, but emerging evidence suggests that glia may also act as vectors for aggregate spread. Accumulation of protein aggregates could compromise the ability of glia to eliminate toxic materials from the brain by disrupting efficient degradation in the phagolysosomal system. A better understanding of phagocytic glial cell deficiencies in the disease state could help to identify novel therapeutic targets for multiple neurological disorders. This study reports that mutant huntingtin (mHTT) aggregates impair glial responsiveness to injury and capacity to degrade neuronal debris in male and female adult Drosophila expressing the gene that causes Huntington's disease (HD). mHTT aggregate formation in neurons impairs engulfment and clearance of injured axons and causes accumulation ofphagolysosomes in glia. Neuronal mHTT expression induces upregulation of key innate immunity and phagocytic genes, some of which were found to regulate mHTT aggregate burden in the brain. Finally, a forward genetic screen revealed Rab10 as a novel component of Draper-dependent phagocytosis that regulates mHTT aggregate transmission from neurons to glia. These data suggest that glial phagocytic defects enable engulfed mHTT aggregates to evade lysosomal degradation and acquire prion-like characteristics. Together, these findings reveal new mechanisms that enhance understanding of the beneficial and potentially harmful effects of phagocytic glia in HD and potentially other neurodegenerative diseases. |
| Hopkins, B. R., Angus-Henry, A., Kim, B. Y., Carlisle, J. A., Thompson, A., Kopp, A. (2024). Decoupled evolution of the Sex Peptide gene family and Sex Peptide Receptor in Drosophilidae. Proc Natl Acad Sci U S A, 121(3):e2312380120 PubMed ID: 38215185
Summary: Across internally fertilising species, males transfer ejaculate proteins that trigger wide-ranging changes in female behaviour and physiology. Much theory has been developed to explore the drivers of ejaculate protein evolution. The accelerating availability of high-quality genomes now allows testing how these proteins are evolving at fine taxonomic scales. Genomes were used from 264 species to chart the evolutionary history of Sex Peptide (SP), a potent regulator of female post-mating responses in Drosophila melanogaster. It is infered that SP first evolved in the Drosophilinae subfamily and has since followed markedly different evolutionary trajectories in different lineages. Outside of the Sophophora-Lordiphosa, SP exists largely as a single-copy gene with independent losses in several lineages. Within the Sophophora-Lordiphosa, the SP gene family has repeatedly and independently expanded. Up to seven copies, collectively displaying extensive sequence variation, are present in some species. Despite these changes, SP expression remains restricted to the male reproductive tract. Alongside, considerable interspecific variation was documented in the presence and morphology of seminal microcarriers that, despite the critical role SP plays in microcarrier assembly in D. melanogaster, appears to be independent of changes in the presence/absence or sequence of SP. Evidence is provided that SP's evolution is decoupled from that of its receptor, Sex Peptide Receptor, in which no evidence was detected of correlated diversifying selection. Collectively, this work describes the divergent evolutionary trajectories that a novel gene has taken following its origin and finds a surprisingly weak coevolutionary signal between a supposedly sexually antagonistic protein and its receptor. | Monier, M., Nuez, I., Borne, F., Courtier-Orgogozo, V. (2024). Higher evolutionary dynamics of gene copy number for Drosophila glue genes located near short repeat sequences. J BMC ecology and evolution, 24(1):18 PubMed ID: 38308233
Summary: During evolution, genes can experience duplications, losses, inversions and gene conversions. Why certain genes are more dynamic than others is poorly understood. This study examined how several Sgs genes encoding glue proteins, which make up a bioadhesive that sticks the animal during metamorphosis, have evolved in Drosophila species. This study examined high-quality genome assemblies of 24 Drosophila species to study the evolutionary dynamics of four glue genes that are present in D. melanogaster and are part of the same gene family - Sgs7 and Sgs8 - across approximately 30 millions of years. A total of 102 Sgs genes were analyzed and grouped into 4 subfamilies. A new nomenclature for these Sgs genes is presented based on protein sequence conservation, genomic location and presence/absence of internal repeats. Two types of glue genes were uncovered. The first category (Sgs1, Sgs3x, Sgs3e) showed a few gene losses but no duplication, no local inversion and no gene conversion. The second group (Sgs3b, Sgs7, Sgs8) exhibited multiple events of gene losses, gene duplications, local inversions and gene conversions. These data suggest that the presence of short "new glue" genes near the genes of the latter group may have accelerated their dynamics. This comparative analysis suggests that the evolutionary dynamics of glue genes is influenced by genomic context. This molecular, phylogenetic and comparative analysis of the four glue genes Sgs1, Sgs3, Sgs7 and Sgs8 provides the foundation for investigating the role of the various glue genes during Drosophila life. |
| Bontonou, G., Saint-Leandre, B., Kafle, T., Baticle, T., Hassan, A., Sanchez-Alcaniz, J. A., Arguello, J. R. (2024). Evolution of chemosensory tissues and cells across ecologically diverse Drosophilids. Nat Commun, 15(1):1047 PubMed ID: 38316749
Summary: Chemosensory tissues exhibit significant between-species variability, yet the evolution of gene expression and cell types underlying this diversity remain poorly understood. To address these questions, transcriptomic analyses were conducted of five chemosensory tissues from six Drosophila species and the findings were integrated with single-cell datasets. While stabilizing selection predominantly shapes chemosensory transcriptomes, thousands of genes in each tissue have evolved expression differences. Genes that have changed expression in one tissue have often changed in multiple other tissues but at different past epochs and are more likely to be cell type-specific than unchanged genes. Notably, chemosensory-related genes have undergone widespread expression changes, with numerous species-specific gains/losses including novel chemoreceptors expression patterns. Sex differences are also pervasive, including a D. melanogaster-specific excess of male-biased expression in sensory and muscle cells in its forelegs. Together, these analyses provide new insights for understanding evolutionary changes in chemosensory tissues at both global and individual gene levels. | Nunes, W. V. B., de Oliveira, D. S., Dias, G. R., Carvalho, A. B., Caruso I, P., Biselli, J. M., Guegen, N., Akkouche, A., Burlet, N., Vieira, C., Carareto, C. M. A. (2023). A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH). G3 (Bethesda), PubMed ID: 38156703
Summary: Odysseus (OdsH) was the first speciation gene described in Drosophila related to hybrid sterility in offspring of mating between D. mauritiana and D. simulans. Its origin is attributed to the duplication of the gene unc-4 in the subgenus Sophophora. By using a much larger sample of Drosophilidae species, this study showed that contrary to what has been previously proposed, OdsH origin occurred 62 million years ago. Evolutionary rates, expression and transcription factor binding sites of OdsH evidence that it may have rapidly experienced neofunctionalization in male sexual functions. Furthermore, the analysis of the OdsH peptide allowed the identification of mutations of D. mauritiana that could result in incompatibility in hybrids. In order to find if OdsH could be related to hybrid sterility, beyond Sophophora, the expression of OdsH was explored in D. arizonae and D. mojavensis, a pair of sister species with incomplete reproductive isolation. THE data indicated that OdsH expression is not atypical in their male-sterile hybrids. In conclusion, it is proposed that the origin of OdsH occurred earlier than previously proposed, followed by neofunctionalization. These results also suggested that its role as a speciation gene might be restricted to D. mauritiana and D. simulans. |
Friday September 13th - Genes, Enzymes and Protein Expression, Evolution, Structure and Function |
| Ozoe, Y., Nakao, T., Kondo, S., Yoshioka, Y., Ozoe, F., Banba, S. (2024). Knock-in mutagenesis in Drosophila Rdl underscores the critical role of the conserved M3 glycine in mediating the actions of broflanilide and isocycloseram on GABA receptors. Pesticide biochemistry and physiology, 199:105776 PubMed ID: 38458683
Summary: γ-Aminobutyric acid receptors (GABARs) are crucial targets for pest control chemicals, including meta-diamide and isoxazoline insecticides, which act as negative allosteric modulators of insect GABARs. Previous cell-based assays have indicated that amino acid residues in the transmembrane cavity between adjacent subunits of Drosophila Rdl GABAR (i.e., Ile276, Leu280, and Gly335) are involved in mediating the action of meta-diamides. In this study, to confirm this result at the organismal level, CRISPR/Cas9-mediated genome editing was used: six transgenic Drosophila strains were generated carrying substitutions in these amino acid residues, and their sensitivity to broflanilide and isocycloseram was investigated. Flies homozygous for the I276F mutation did not exhibit any change in sensitivity to the tested insecticides compared to the control flies. Conversely, I276C homozygosity was lethal, and heterozygous flies exhibited ∼2-fold lower sensitivity to broflanilide than the control flies. Flies homozygous for the L280C mutation survived into adulthood but exhibited infertility. Both heterozygous and homozygous L280C flies exhibited ∼3- and ∼20-fold lower sensitivities to broflanilide and isocycloseram, respectively, than the control flies. The reduction in sensitivity to isocycloseram in L280C flies diminished to ∼3-fold when treated with piperonyl butoxide. Flies homozygous for the G335A mutation reached the adult stage. However, they were sterile, had small bodies, and exhibited reduced locomotion, indicating the critical role of Gly335 in RDL function. These flies exhibited markedly increased tolerance to topically applied broflanilide and isocycloseram, demonstrating that the conserved Gly335 is the target of the insecticidal actions of broflanilide and isocycloseram. Considering the significant fitness costs, the Gly335 mutation may not pose a serious risk for the development of resistance in field populations of insect pests. However, more careful studies using insect pests are needed to investigate whether this perspective applies to resistance development under field conditions. | Lee, K. T., Pranoto, I. K. A., Kim, S. Y., Choi, H. J., To, N. B., Chae, H., Lee, J. Y., Kim, J. E., Kwon, Y. V., Nam, J. W. (2024).. Comparative interactome analysis of α-arrestin families in human and Drosophila. Elife, 12 PubMed ID: 38270169
Summary: The α-arrestins form a large family of evolutionally conserved modulators that control diverse signaling pathways, including both G-protein-coupled receptor (GPCR)-mediated and non-GPCR-mediated pathways, across eukaryotes. However, unlike β-arrestins, only a few α-arrestin targets and functions have been characterized. Using affinity purification and mass spectrometry, this study constructed interactomes for 6 human and 12 Drosophila α-arrestins. The resulting high-confidence interactomes comprised 307 and 467 prey proteins in human and Drosophila, respectively. A comparative analysis of these interactomes predicted not only conserved binding partners, such as motor proteins, proteases, ubiquitin ligases, RNA splicing factors, and GTPase-activating proteins, but also those specific to mammals, such as histone modifiers and the subunits of V-type ATPase. Given the manifestation of the interaction between the human α-arrestin, TXNIP, and the histone-modifying enzymes, including HDAC2, this study undertook a global analysis of transcription signals and chromatin structures that were affected by TXNIP knockdown. TXNIP activated targets by blocking HDAC2 recruitment to targets, a result that was validated by chromatin immunoprecipitation assays. Additionally, the interactome for an uncharacterized human α-arrestin ARRDC5 uncovered multiple components in the V-type ATPase, which plays a key role in bone resorption by osteoclasts. This study presents conserved and species-specific protein-protein interaction maps for α-arrestins, which provide a valuable resource for interrogating their cellular functions for both basic and clinical research. |
| Marchesan, E., Nardin, A., Mauri, S., Bernardo, G., Chander, V., Di Paola, S., Chinellato, M., von Stockum, S., Chakraborty, J., Herkenne, S., Basso, V., Schrepfer, E., Marin, O., Cendron, L., Medina, D. L., Scorrano, L., Ziviani, E. (2024). Activation of Ca(2+) phosphatase Calcineurin regulates Parkin translocation to mitochondria and mitophagy in flies. Cell Death Differ, 31(2):217-238 PubMed ID: 38238520
Summary: Selective removal of dysfunctional mitochondria via autophagy is crucial for the maintenance of cellular homeostasis. This event is initiated by the translocation of the E3 ubiquitin ligase Parkin to damaged mitochondria, and it requires the Serine/Threonine-protein kinase PINK1. In a coordinated set of events, PINK1 operates upstream of Parkin in a linear pathway that leads to the phosphorylation of Parkin, Ubiquitin, and Parkin mitochondrial substrates, to promote ubiquitination of outer mitochondrial membrane proteins. Ubiquitin-decorated mitochondria are selectively recruiting autophagy receptors, which are required to terminate the organelle via autophagy. This work shows a previously uncharacterized molecular pathway that correlates the activation of the Ca(2+)-dependent phosphatase Calcineurin to Parkin translocation and Parkin-dependent mitophagy. Calcineurin downregulation or genetic inhibition prevents Parkin translocation to CCCP-treated mitochondria and impairs stress-induced mitophagy, whereas Calcineurin activation promotes Parkin mitochondrial recruitment and basal mitophagy. Calcineurin interacts with Parkin, and promotes Parkin translocation in the absence of PINK1, but requires PINK1 expression to execute mitophagy in MEF cells. Genetic activation of Calcineurin in vivo boosts basal mitophagy in neurons and corrects locomotor dysfunction and mitochondrial respiratory defects of a Drosophila model of impaired mitochondrial functions. This study identifies Calcineurin as a novel key player in the regulation of Parkin translocation and mitophagy. | Kose, C., Cao, X., Dewey, E. B., Malkoç, M., Adebali, O., Sekelsky, J., Lindsey-Boltz, L. A., Sancar, A. (2024). Cross-species investigation into the requirement of XPA for nucleotide excision repair. Nucleic Acids Res, 52(2):677-689 PubMed ID: 37994737
Summary: After reconstitution of nucleotide excision repair (excision repair) with XPA, RPA, XPC, TFIIH, XPF-ERCC1 and |
| Ozcelik, G., Koca, M. S., Sunbul, B., Yilmaz-Atay, F., Demirhan, F., Tiryaki, B., Cilenk, K., Selvi, S., Ozturk, N. (2024). Interactions of drosophila cryptochrome. Photochemistry and photobiology. PubMed ID: 38314442
Summary: This study investigated the intricate regulatory mechanisms underlying the circadian clock in Drosophila, focusing on the light-induced conformational changes in the Cryptochrome (Cry). Upon light exposure, Cry undergoes conformational changes that prompt its binding to Timeless and Jetlag proteins, initiating a cascade crucial for the starting of a new circadian cycle. Cry is subsequently degraded, contributing to the desensitization of the resetting mechanism. The transient and short-lived nature of Cry protein-protein interactions (PPIs), leading to Cry degradation within an hour of light exposure, presents a challenge for comprehensive exploration. To address this, proximity-dependent biotinylation techniques were employed,. This approach enabled the identification of the in vitro Cry interactome in Drosophila S2 cells, uncovering several novel PPIs associated with Cry. Validation of these interactions through a novel co-immunoprecipitation technique enhanced the reliability of these findings. Importantly, this method reveals additional circadian clock- or magnetic field-dependent PPIs involving Cry. | Gonzaaez, C., Martínez-Sanchez, L., Clemente, P., Toivonen, J. M., Arredondo, J. J., Fernandez-Moreno, M., Carrodeguas, J. A. (2024). Dysfunction of Drosophila mitochondrial carrier homolog (Mtch) alters apoptosis and disturbs development. FEBS open bio, 14(2):276-289 PubMed ID: 38013241
Summary: Mitochondrial carrier homologs 1 (MTCH1) and 2 (MTCH2) are orphan members of the mitochondrial transporter family SLC25. Human MTCH1 is also known as presenilin 1-associated protein, PSAP. MTCH2 is a receptor for tBid and is related to lipid metabolism. Both proteins have been recently described as protein insertases of the outer mitochondrial membrane. This study depleted Mtch in Drosophila and shows here that mutant flies are unable to complete development, showing an excess of apoptosis during pupation; this observation was confirmed by RNAi in Schneider cells. These findings are contrary to what has been described in humans. The implications in view of recent reports concerning the function of these proteins are discussed. |
Thursday, September 12h - Adult Neural, Structure, Development and Functions |
| Wu, C., Wang, J., Luo, X., Wang, B., Zhang, X., Song, Y., Zhang, K., Zhang, X., Sun, M. (2024). Lead exposure induced transgenerational developmental neurotoxicity by altering genome methylation in Drosophila melanogaster. Ecotoxicol Environ Saf, 271:115991 PubMed ID: 38237395
Summary: Heavy metal toxicity is a significant global health concern, with particular attention given to lead (Pb) exposure due to its adverse effects on cognitive development, especially in children exposed to low concentrations. While Pb neurotoxicity has been extensively studied, the analysis and molecular mechanisms underlying the transgenerational effects of Pb exposure-induced neurotoxicity remain poorly understood. This study utilized Drosophila, a powerful developmental animal model, to investigate this phenomenon. The findings demonstrated that Pb exposure during the developmental stage had a profound effect on the neurodevelopment of F0 fruit flies. Specifically, it was observed that a loss of correlation between the terminal motor area and muscle fiber area, along with an increased frequency of the β-lobe midline crossing phenotype in mushroom bodies. Western blot analysis indicated altered expression levels of synaptic vesicle proteins, with a decrease in Synapsin (SYN) and an increase in Bruchpilot (BRP) expression, suggesting changes in synaptic vesicle release sites. These findings were corroborated by electrophysiological data, showing an increase in the amplitude of evoked excitatory junctional potential (EJP) and an increase in the frequency of spontaneous excitatory junctional potential (mEJP) following Pb exposure. Importantly, these results further confirmed that the developmental neurotoxicity resulting from grandparental Pb exposure exhibited a transgenerational effect. The F3 offspring displayed neurodevelopmental defects, synaptic function abnormalities, and repetitive behavior despite lacking direct Pb exposure. MeDIP-seq analysis further revealed significant alterations in DNA methylation levels in several neurodevelopmental associated genes (eagle, happyhour, neuroglian, bazooka, and spinophilin) in the F3 offspring exposed to Pb. These findings suggest that DNA methylation modifications may underlie the inheritance of acquired phenotypic traits resulting from environmental Pb exposure. | Mussells Pires, P., Zhang, L., Parache, V., Abbott, L. F., Maimon, G. (2024). Converting an allocentric goal into an egocentric steering signal. Nature, 626(8000):808-818 PubMed ID: 38326612
Summary: Neuronal signals that are relevant for spatial navigation have been described in many species. However, a circuit-level understanding of how such signals interact to guide navigational behaviour is lacking. This study characterized a neuronal circuit in the Drosophila central complex that compares internally generated estimates of the heading and goal angles of the fly-both of which are encoded in world-centred (allocentric) coordinates-to generate a body-centred (egocentric) steering signal. Past work has suggested that the activity of EPG neurons represents the fly's moment-to-moment angular orientation, or heading angle, during navigation. An animal's moment-to-moment heading angle, however, is not always aligned with its goal angle-that is, the allocentric direction in which it wishes to progress forward. This study describes FC2 cells, a second set of neurons in the Drosophila brain with activity that correlates with the fly's goal angle. Focal optogenetic activation of FC2 neurons induces flies to orient along experimenter-defined directions as they walk forward. EPG and FC2 neurons connect monosynaptically to a third neuronal class, PFL3 cells. This study found that individual PFL3 cells show conjunctive, spike-rate tuning to both the heading angle and the goal angle during goal-directed navigation. Informed by the anatomy and physiology of these three cell classes, a model was developed that explains how this circuit compares allocentric heading and goal angles to build an egocentric steering signal in the PFL3 output terminals. Quantitative analyses and optogenetic manipulations of PFL3 activity support the model. Finally, using a new navigational memory task, it was shown that flies expressing disruptors of synaptic transmission in subsets of PFL3 cells have a reduced ability to orient along arbitrary goal directions, with an effect size in quantitative accordance with the prediction of this model. The biological circuit described here reveals how two population-level allocentric signals are compared in the brain to produce an egocentric output signal that is appropriate for motor control. |
| Pospisil, D.A., Aragon, M.J., Dorkenwald, S., Matsliah, A. ..., Jefferis, G.S.X.E., Murth,y M., Pillow, J.W. (2024). From connectome to effectome: learning the causal interaction map of the fly brain.. bioRxiv PubMed ID: 37961285
Summary: A long-standing goal of neuroscience is to obtain a causal model of the nervous system. This would allow neuroscientists to explain animal behavior in terms of the dynamic interactions between neurons. The recently reported whole-brain fly connectome specifies the synaptic paths by which neurons can affect each other but not whether, or how, they do affect each other in vivo. To overcome this limitation, a novel combined experimental and statistical strategy was introduced for efficiently learning a causal model of the fly brain was introduced, which is refered to as the 'effectome'. Specifically, an estimator is proposed for a dynamical systems model of the fly brain that uses stochastic optogenetic perturbation data to accurately estimate causal effects and the connectome as a prior to drastically improve estimation efficiency. Then the connectome was analyzed to propose circuits that have the greatest total effect on the dynamics of the fly nervous system. It was discovered that, fortunately, the dominant circuits significantly involve only relatively small populations of neurons—thus imaging, stimulation, and neuronal identification are feasible. Intriguingly, this approach also re-discovers known circuits and generates testable hypotheses about their dynamics. Overall, this analyses of the connectome provide evidence that global dynamics of the fly brain are generated by a large collection of small and often anatomically localized circuits operating, largely, independently of each other. This in turn implies that a causal model of a brain, a principal goal of systems neuroscience, can be feasibly obtained in the fly. | Mitra, R., Richhariya, S., Hasan, G. (2024). Orai-mediated calcium entry determines activity of central dopaminergic neurons by regulation of gene expression.. Elife, 12 PubMed ID: 38289659
Summary: Maturation and fine-tuning of neural circuits frequently require neuromodulatory signals that set the excitability threshold, neuronal connectivity, and synaptic strength. This study presents a mechanistic study of how neuromodulator-stimulated intracellular Ca(2+) signals, through the store-operated Ca(2+) channel Orai, regulate intrinsic neuronal properties by control of developmental gene expression in flight-promoting central dopaminergic neurons (fpDANs). The fpDANs receive cholinergic inputs for release of dopamine at a central brain tripartite synapse that sustains flight. Cholinergic inputs act on the muscarinic acetylcholine receptor to stimulate intracellular Ca(2+) release through the endoplasmic reticulum (ER) localised inositol 1,4,5-trisphosphate receptor followed by ER-store depletion and Orai-mediated store-operated Ca(2+) entry (SOCE). Analysis of gene expression in fpDANs followed by genetic, cellular, and molecular studies identified Orai-mediated Ca(2+) entry as a key regulator of excitability in fpDANs during circuit maturation. SOCE activates the transcription factor trithorax-like (Trl), which in turn drives expression of a set of genes, including Set2, that encodes a histone 3 lysine 36 methyltransferase (H3K36me3). Set2 function establishes a positive feedback loop, essential for receiving neuromodulatory cholinergic inputs and sustaining SOCE. Chromatin-modifying activity of Set2 changes the epigenetic status of fpDANs and drives expression of key ion channel and signalling genes that determine fpDAN activity. Loss of activity reduces the axonal arborisation of fpDANs within the MB lobe and prevents dopamine release required for the maintenance of long flight. |
| Lu, S., Qian, C. S., Grueber, W. B. (2024). Mechanisms of gas sensing by internal sensory neurons in Drosophila larvae. bioRxiv, PubMed ID: 38293088
Summary: Internal sensory neurons monitor the chemical and physical state of the body, providing critical information to the central nervous system for maintaining homeostasis and survival. A population of larval Drosophila sensory neurons, tracheal dendrite (td) neurons, elaborate dendrites along respiratory organs and may serve as a model for elucidating the cellular and molecular basis of chemosensation by internal neurons. It was found that td neurons respond to decreases in O(2) levels and increases in CO(2) levels. The roles of atypical soluble guanylyl cyclases (Gycs) and a gustatory receptor (Gr) in mediating these responses. Gyc88E/Gyc89Db were necessary for responses to hypoxia, and that Gr28b was necessary for responses to CO(2). Targeted expression of Gr28b isoform c in td neurons rescued responses to CO(2) in mutant larvae and also induced ectopic sensitivity to CO(2) in the td network. Gas-sensitive td neurons were activated when larvae burrowed for a prolonged duration, demonstrating a natural-like feeding condition in which td neurons are activated. Together, this work identifies two gaseous stimuli that are detected by partially overlapping subsets of internal sensory neurons, and establishes roles for Gyc88E/Gyc89Db in the detection of hypoxia, and Gr28b in the detection of CO(2). | Jurgensen, A. M., Sakagiannis, P., Schleyer, M., Gerber, B., Nawrot, M. P. (2024). Prediction error drives associative learning and conditioned behavior in a spiking model of Drosophila larva. iScience, 27(1):108640 PubMed ID: 38292165
Summary: Predicting reinforcement from sensory cues is beneficial for goal-directed behavior. In insect brains, underlying associations between cues and reinforcement, encoded by dopaminergic neurons, are formed in the mushroom body. A spiking model of the Drosophila larva mushroom body is proposed. It includes a feedback motif conveying learned reinforcement expectation to dopaminergic neurons, which can compute prediction error as the difference between expected and present reinforcement. This can serve as a driving force in learning. When combined with synaptic homeostasis, this model accounts for theoretically derived features of acquisition and loss of associations that depend on the intensity of the reinforcement and its temporal proximity to the cue. From modeling olfactory learning over the time course of behavioral experiments and simulating the locomotion of individual larvae toward or away from odor sources in a virtual environment, it is concluded that learning driven by prediction errors can explain larval behavior. |
Wednesday, September 12th - Chromatin |
| Brown, J. L., Zhang, L., Rocha, P. P., Kassis, J. A., Sun, M. A. (2023). Polycomb protein binding and looping mediated by Polycomb Response Elements in the ON transcriptional state. bioRxiv, PubMed ID: 38076900
Summary: Polycomb group proteins (PcG) mediate epigenetic silencing of important developmental genes and other targets. In Drosophila, canonical PcG-target genes contain Polycomb Response Elements (PREs) that recruit PcG protein complexes including PRC2 that trimethylates H3K27 forming large H3K27me3 domains. In the OFF transcriptional state, PREs loop with each other and this looping strengthens silencing. This study addressed the question of what PcG proteins bind to PREs when canonical PcG target genes are expressed, and whether PREs loop when these genes are ON. The data show that the answer to this question is PRE-specific but general conclusions can be made. First, within a PcG-target gene, some regulatory DNA can remain covered with H3K27me3 and PcG proteins remain bound to PREs in these regions. Second, when PREs are within H3K27ac domains, PcG-binding decreases, however, this depends on the protein and PRE. The DNA binding protein GAF, and the PcG protein Ph, remain at PREs even when other PcG proteins are greatly depleted. In the ON state, PREs can still loop with each other, but also form loops with presumptive enhancers. These data support the model that, in addition to their role in PcG silencing, PREs can act as "promoter-tethering elements" mediating interactions between promoter proximal PREs and distant enhancers. | Romanov, S. E., Shloma, V. V., Maksimov, D. A., Koryakov, D. E. (2023). SetDB1 and Su(var)3-9 are essential for late stages of larval development of Drosophila melanogaster. Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology, 31(4):35 PubMed ID: 38099968
Summary: Methylation of H3K9 histone residue is a marker of gene silencing in eukaryotes. Three enzymes responsible for adding this modification - G9a, SetDB1/Egg, and Su(var)3-9 - are known in Drosophila. To understand how simultaneous mutations of SetDB1 and Su(var)3-9 may affect the fly development, appropriate combinations were obtained. Double mutants egg; Su(var)3-9 displayed pronounced embryonic lethality, slower larval growth and died before or during metamorphosis. Analysis of transcription in larval salivary glands and wing imaginal disks indicated that the effect of double mutation is tissue-specific. In salivary gland chromosomes, affected genes display low H3K9me2 enrichment and are rarely bound by SetDB1 or Su(var)3-9. It is supposed that each of these enzymes directly or indirectly controls its own set of gene targets in different organs, and double mutation results in an imbalanced developmental program. This also indicates that SetDB1 and Su(var)3-9 may affect transcription via H3K9-independent mechanisms. Unexpectedly, in double and triple mutants, amount of di- and tri-methylated H3K9 is drastically reduced, but not completely absent. It is hypothesized that this residual methylation implies the existence of additional H3K9-specific methyltransferase in Drosophila. |
| Zhu, J. Y., Lee, H., Huang, X., van de Leemput, J., Han, Z. (2023). Distinct Roles for COMPASS Core Subunits Set1, Trx, and Trr in the Epigenetic Regulation of Drosophila Heart Development. Int J Mol Sci, 24(24) PubMed ID: 38139143
Summary: Highly evolutionarily conserved multiprotein complexes termed Complex of Proteins Associated with Set1 (COMPASS) are required for histone 3 lysine 4 (H3K4) methylation. Drosophila Set1, Trx, and Trr form the core subunits of these complexes. This study showed that flies deficient in any of these three subunits demonstrated high lethality at eclosion (emergence of adult flies from their pupal cases) and significantly shortened lifespans for the adults that did emerge. Silencing Set1, trx, or trr in the heart led to a reduction in H3K4 monomethylation (H3K4me1) and dimethylation (H3K4me2), reflecting their distinct roles in H3K4 methylation. Furthermore, the gene expression patterns regulated by Set1, Trx, and Trr were studied. Each of the COMPASS core subunits controls the methylation of different sets of genes, with many metabolic pathways active early in development and throughout, while muscle and heart differentiation processes were methylated during later stages of development. Taken together, these findings demonstrate the roles of COMPASS series complex core subunits Set1, Trx, and Trr in regulating histone methylation during heart development and, given their implication in congenital heart diseases, inform research on heart disease. | Vizjak, P., Kamp, D., Hepp, N., Scacchetti, A., Pisfil, M. G., Bartho, J., Halic, M., Becker, P. B., Smolle, M., Stigler, J., Mueller-Planitz, F. (2023). ISWI catalyzes nucleosome sliding in condensed nucleosome arrays. bioRxiv, PubMed ID: 38106060
Summary: How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. This study investigated these challenges using the Drosophila ISWI remodeling ATPase, which slides nucleosomes along DNA. Folding of chromatin fibers did not affect sliding in vitro. Catalytic rates were also comparable in- and outside of chromatin condensates. ISWI cross-links and thereby stiffens condensates, except when ATP hydrolysis is possible. Active hydrolysis is also required for ISWI's mobility in condensates. Energy from ATP hydrolysis therefore fuels ISWI's diffusion through chromatin and prevents ISWI from cross-linking chromatin. Molecular dynamics simulations of a 'monkey-bar' model in which ISWI grabs onto neighboring nucleosomes, then withdraws from one before rebinding another in an ATP hydrolysis-dependent manner qualitatively agree with the data. It is speculated that 'monkey-bar' mechanisms could be shared with other chromatin factors and that changes in chromatin dynamics caused by mutations in remodelers could contribute to pathologies. |
| Pollex, T., Marco-Ferreres, R., Ciglar, L., Ghavi-Helm, Y., Rabinowitz, A., Viales, R. R., Schaub, C., Jankowski, A., Girardot, C., Furlong, E. E. M. (2023).. Chromatin gene-gene loops support the cross-regulation of genes with related function. Mol Cell, PubMed ID: 38157845
Summary: Chromatin loops between gene pairs have been observed in diverse contexts in both flies and vertebrates. Combining high-resolution Capture-C, DNA fluorescence in situ hybridization, and genetic perturbations, this study dissected the functional role of three loops between genes with related function during Drosophila embryogenesis. By mutating the loop anchor (but not the gene) or the gene (but not loop anchor), loop formation and gene expression were disentangled, and the 3D proximity of paralogous gene loci supports their co-regulation. Breaking the loop leads to either an attenuation or enhancement of expression and perturbs their relative levels of expression and cross-regulation. Although many loops appear constitutive across embryogenesis, their function can change in different developmental contexts. Taken together, these results indicate that chromatin gene-gene loops act as architectural scaffolds that can be used in different ways in different contexts to fine-tune the coordinated expression of genes with related functions and sustain their cross-regulation. | Kurshakova, M. M., Yakusheva, Y. A., Georgieva, S. G. (2024). TREX-2-ORC Complex of D. melanogaster Participates in Nuclear Export of Histone mRNA. Doklady Biochemistry and biophysics, 514(1):11-15 PubMed ID: 38189888
Summary: The TREX-2-ORC protein complex of D. melanogaster is necessary for the export of the bulk of synthesized poly(A)-containing mRNA molecules from the nucleus to the cytoplasm through the nuclear pores. However, the role of this complex in the export of other types of RNA remains unknown. This study has shown that TREX-2-ORC participates in the nuclear export of histone mRNAs: it associates with histone mRNPs, binds to histone H3 mRNA at the 3'-terminal part of the coding region, and participates in the export of histone mRNAs from the nucleus to the cytoplasm. |
Tuesday, September 10th - Disease Models |
| Atrian, F., Ramirez, P., De Mange, J., Marquez, M., Gonzalez, E. M., Minaya, M., Karch, C. M., Frost, B. (2024). m6A-dependent circular RNA formation mediates tau-induced neurotoxicity. bioRxiv, PubMed ID: 38328044
Summary: Circular RNAs (circRNAs), covalently closed RNA molecules that form due to back-splicing of RNA transcripts, have recently been implicated in Alzheimer's disease and related tauopathies. circRNAs are regulated by N(6)-methyladenosine (m(6)A) RNA methylation, can serve as "sponges" for proteins and RNAs, and can be translated into protein via a cap-independent mechanism. Mechanisms underlying circRNA dysregulation in tauopathies and causal relationships between circRNA and neurodegeneration are currently unknown. The current study aimed to determine whether pathogenic forms of tau drive circRNA dysregulation and whether such dysregulation causally mediates neurodegeneration. circRNAs were identified that are differentially expressed in the brain of a Drosophila model of tauopathy and in induced pluripotent stem cell (iPSC)-derived neurons carrying a tau mutation associated with autosomal dominant tauopathy. Drosophila was leveraged to discover that depletion of circular forms of muscleblind (circMbl), a circRNA that is particularly abundant in brains of tau transgenic Drosophila, significantly suppresses tau neurotoxicity, suggesting that tau-induced circMbl elevation is neurotoxic. A general elevation of m(6)A RNA methylation and circRNA methylation were detected in tau transgenic Drosophila, and tau-induced m(6)A methylation was found to be a mechanistic driver of circMbl formation. Interestingly, it was found that circRNA and m(6)A RNA accumulate within nuclear envelope invaginations of tau transgenic Drosophila and in iPSC-derived cerebral organoid models of tauopathy. Taken together, othese studies add critical new insight into the mechanisms underlying circRNA dysregulation in tauopathy and identify m(6)A-modified circRNA as a causal factor contributing to neurodegeneration. These findings add to a growing literature implicating pathogenic forms of tau as drivers of altered RNA metabolism. | Chvilicek, M. M., Seguin, A., Lathen, D. R., Titos, I., Cummins-Beebee, P. N., Pabon, M. A., Miscevic, M., Nickel, E., Merrill, C. B., Rodan, A. R., Rothenfluh, A. (2024). Large analysis of genetic manipulations reveals an inverse correlation between initial alcohol resistance and rapid tolerance phenotypes. Genes Brain Behav, 23(1):e12884 PubMed ID: 38968320
Summary: Tolerance occurs when, following an initial experience with a substance, more of the substance is required subsequently to induce identical behavioral effects. Tolerance is not well-understood, and numerous researchers have turned to model organisms, particularly Drosophila melanogaster, to unravel its mechanisms. Flies have high translational relevance for human alcohol responses, and there is substantial overlap in disease-causing genes between flies and humans, including those associated with Alcohol Use Disorder. Numerous Drosophila tolerance mutants have been described; however, approaches used to identify and characterize these mutants have varied across time and labs and have mostly disregarded any impact of initial resistance/sensitivity to ethanol on subsequent tolerance development. These analyzed published data to uncover an inverse correlation between initial ethanol resistance and tolerance phenotypes. This inverse correlation suggests that initial resistance phenotypes can explain many 'perceived' tolerance phenotypes, thus classifying such mutants as 'secondary' tolerance mutants. Additionally, it was shown that tolerance should be measured as a relative increase in time to sedation between an initial and second exposure rather than an absolute change in time to sedation. Finally, based on this analysis, a method is provided for using a linear regression equation to assess the residuals of potential tolerance mutants. These residuals provide predictive insight into the likelihood of a mutant being a 'primary' tolerance mutant, where a tolerance phenotype is not solely a consequence of initial resistance, and a framework is offered for understanding the relationship between initial resistance and tolerance. |
| Brown, E. B., Lloyd, E., Martin-Pena, A., McFarlane, S., Dahanukar, A., Keene, A. C. (2024). Aging is associated with a modality-specific decline in taste.. bioRxiv, PubMed ID: 38352472
Summary: Deficits in chemosensory processing are associated with healthy aging, as well as numerous neurodegenerative disorders, including Alzheimer's Disease (AD). In many cases, chemosensory deficits are harbingers of neurodegenerative disease, and understanding the mechanistic basis for these changes may provide insight into the fundamental dysfunction associated with aging and neurodegeneration. The fruit fly, Drosophila melanogaster , is a powerful model for studying chemosensation, aging, and aging-related pathologies, yet the effects of aging and neurodegeneration on chemosensation remain largely unexplored in this model, particularly with respect to taste. To determine whether the effects of aging on taste are conserved in flies, the response of flies to different appetitive tastants was compared. Aging impaired response to sugars, but not medium-chain fatty acids that are sensed by a shared population of neurons, revealing modality-specific deficits in taste. Selective expression of the human amyloid beta (Aβ) 1-42 peptide bearing the Arctic mutation (E693E) associated with early onset AD in the neurons that sense sugars and fatty acids phenocopies the effects of aging, suggesting that the age-related decline in response is localized to gustatory neurons. Functional imaging of gustatory axon terminals revealed reduced response to sugar, but not fatty acids. Axonal innervation of the fly taste center was largely intact in aged flies, suggesting that reduced sucrose response does not derive from neurodegeneration. Conversely, expression of the amyloid peptide in sweet-sensing taste neurons resulted in reduced innervation of the primary fly taste center. A comparison of transcript expression within the sugar-sensing taste neurons revealed age-related changes in 66 genes, including a reduction in odorant-binding protein class genes that are also expressed in taste sensilla. Together, these findings suggest that deficits in taste detection may result from signaling pathway-specific changes, while different mechanisms underly taste deficits in aged and AD model flies. Overall, this work provides a model to examine cellular deficits in neural function associated with aging and AD. | Luo, M., Yuan, Q., Xie, Y., Mai, M., Song, W., Wang, Y., Shi, H., Xia, E., Guo, H. (2024). Yo-yo Dieting Delays Male Drosophila melanogaster Aging Through Enhanced Mitochondrial Function, Relative to Sustained High-Calorie Diet Feeding. The journals of gerontology Series A, Biological sciences and medical sciences, PubMed ID: 38198696
Summary: Weight regain subsequent to weight reduction resulting from dietary interventions represents a prevalent phenomenon recognized as "Yo-yo dieting." However, the impact of prolonged Yo-yo dieting on health, especially in relation to the aging process, remains poorly understood. This study aimed to investigate the influence of Yo-yo dieting on the aging process in male Drosophila melanogaster that have been exposed to a high-calorie (HC) diet. Fruit flies were fed with either a consistent HC diet or an alternating regimen of HC and low-calorie diets every three days (referred to as "Yo-yo dieting") for a total of 24 days. Biochemical assays were utilized to quantify levels of oxidative stress and activities of the mitochondrial respiratory chain complexes. The frozen section staining method was employed to assess the presence of lipid droplets, reactive oxygen species, cellular viability, and mitochondrial abundance in tissues was examined. Additionally, the expression of key regulators involved in mitochondrial dynamics and biogenic signaling pathways. Yo-yo dieting resulted in an extension of the fruit flies' lifespan, concomitant with reduced body weight, decreased body protein content, and lower triglyceride levels compared to continuous a HC diet feeding. Furthermore, Yo-yo dieting ameliorated impairments in motility and intestinal barrier function. Importantly, it improved mitochondrial function and upregulated the expression of essential mitochondrial fusion proteins, namely mitofusin 1 and mitofusin 2, optic atrophy 1 (Opa1), and peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α). Therefore, the practice of Yo-yo dieting extends the lifespan of fruit flies by modulating mitochondrial dynamics and the associated biogenic signaling pathways. |
| Bukhari, H., Nithianandam, V., Battaglia, R. A., Cicalo, A., Sarkar, S., Comjean, A., Hu, Y., Leventhal, M. J., Dong, X., Feany, M. B. (2024). Transcriptional programs mediating neuronal toxicity and altered glial-neuronal signaling in a Drosophila knock-in tauopathy model. bioRxiv, PubMed ID: 38352559
Summary: Missense mutations in the gene encoding the microtubule-associated protein tau cause autosomal dominant forms of frontotemporal dementia. Multiple models of frontotemporal dementia based on transgenic expression of human tau in experimental model organisms, including Drosophila, have been described. These models replicate key features of the human disease, but do not faithfully recreate the genetic context of the human disorder. This study used CRISPR-Cas mediated gene editing to model frontotemporal dementia caused by the tau P301L mutation by creating the orthologous mutation, P251L, in the endogenous Drosophila tau gene. Flies heterozygous or homozygous for tau P251L display age-dependent neurodegeneration, metabolic defects and accumulate DNA damage in affected neurons. To understand the molecular events promoting neuronal dysfunction and death in knock-in flies single-cell RNA sequencing was used on approximately 130,000 cells from brains of tau P251L mutant and control flies. Expression of disease-associated mutant tau altered gene expression cell autonomously in all neuronal cell types identified and non-cell autonomously in glial cells. Cell signaling pathways, including glial-neuronal signaling, were broadly dysregulated as were brain region and cell-type specific protein interaction networks and gene regulatory programs. In summary, this study presents a genetic model of tauopathy, which faithfully recapitulates the genetic context and phenotypic features of the human disease and use the results of comprehensive single cell sequencing analysis to outline pathways of neurotoxicity and highlight the role of non-cell autonomous changes in glia. | Davis, G. H., Zaya, A., Pearce, M. M. P. (2024). Impairment of the glial phagolysosomal system drives prion-like propagation in a Drosophila model of Huntington's disease. bioRxiv, PubMed ID: 38370619
Summary: Protein misfolding, aggregation, and spread through the brain are primary drivers of neurodegenerative diseases pathogenesis. Phagocytic glia are responsible for regulating the load of pathogenic protein aggregates in the brain, but emerging evidence suggests that glia may also act as vectors for aggregate spread. Accumulation of protein aggregates could compromise the ability of glia to eliminate toxic materials from the brain by disrupting efficient degradation in the phagolysosomal system. A better understanding of phagocytic glial cell deficiencies in the disease state could help to identify novel therapeutic targets for multiple neurological disorders. This study reports that mutant huntingtin (mHTT) aggregates impair glial responsiveness to injury and capacity to degrade neuronal debris in male and female adult Drosophila expressing the gene that causes Huntington's disease (HD). mHTT aggregate formation in neurons impairs engulfment and clearance of injured axons and causes accumulation of phagolysosomes in glia. Neuronal mHTT expression induces upregulation of key innate immunity and phagocytic genes, some of which were found to regulate mHTT aggregate burden in the brain. Finally, a forward genetic screen revealed Rab10 as a novel component of Draper-dependent phagocytosis that regulates mHTT aggregate transmission from neurons to glia. These data suggest that glial phagocytic defects enable engulfed mHTT aggregates to evade lysosomal degradation and acquire prion-like characteristics. Together, these findings reveal new mechanisms that enhance understanding of the beneficial and potentially harmful effects of phagocytic glia in HD and potentially other neurodegenerative diseases. |
Monday, September 9th - Transcriptional Regulation |
| Hunt, G., Vaid, R., Pirogov, S., Pfab, A., Ziegenhain, C., Sandberg, R., Reimegard, J., Mannervik, M. (2024). Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network. Genome Biol, 25(1):2 PubMed ID: 38166964
Summary: Formation of tissue-specific transcriptional programs underlies multicellular development, including dorsoventral (DV) patterning of the Drosophila embryo. This involves interactions between transcriptional enhancers and promoters in a chromatin context, but how the chromatin landscape influences transcription is not fully understood. This study comprehensively resolved differential transcriptional and chromatin states during Drosophila DV patterning. RNA Polymerase II pausing is established at DV promoters prior to zygotic genome activation (ZGA), that pausing persists irrespective of cell fate, but that release into productive elongation is tightly regulated and accompanied by tissue-specific P-TEFb recruitment. DV enhancers acquire distinct tissue-specific chromatin states through CBP-mediated histone acetylation that predict the transcriptional output of target genes, whereas promoter states are more tissue-invariant. Transcriptome-wide inference of burst kinetics in different cell types revealed that while DV genes are generally characterized by a high burst size, either burst size or frequency can differ between tissues. The data suggest that pausing is established by pioneer transcription factors prior to ZGA and that release from pausing is imparted by enhancer chromatin state to regulate bursting in a tissue-specific manner in the early embryo. These results uncover how developmental patterning is orchestrated by tissue-specific bursts of transcription from Pol II primed promoters in response to enhancer regulatory cues. | Akpoghiran, O., Afonso, D. J. S., Zhang, Y., Koh, K. (2023). TARANIS interacts with VRILLE and PDP1 to modulate the circadian transcriptional feedback mechanism in Drosophila. bioRxiv, PubMed ID: 38076905
Summary: The molecular clock that generates daily rhythms of behavior and physiology consists of interlocked transcription-translation feedback loops. In Drosophila, the primary feedback loop involving the CLOCK-CYCLE transcriptional activators and the PERIOD-TIMELESS transcriptional repressors is interlocked with a secondary loop involving VRILLE (VRI) and PAR DOMAIN PROTEIN 1 (PDP1), a repressor and activator of Clock transcription, respectively. Whereas extensive studies have found numerous transcriptional, translational, and post-translational modulators of the primary loop, relatively little is known about the secondary loop. In this study, using male and female flies as well as cultured cells, this study demonstrated that TARANIS (TARA), a Drosophila homolog of the TRIP-Br/SERTAD family of transcriptional coregulators, functions with VRI and PDP1 to modulate the circadian period and rhythm strength. Knocking down tara reduces rhythm amplitude and can shorten the period length, while overexpressing TARA lengthens the circadian period. Additionally, tara mutants exhibit reduced rhythmicity and lower expression of the PDF neuropeptide. TARA can form a physical complex with VRI and PDP1, enhancing their repressor and activator functions, respectively. The conserved SERTA domain of TARA is required to regulate the transcriptional activity of VRI and PDP1, and its deletion leads to reduced locomotor rhythmicity. Consistent with TARA's role in enhancing VRI and PDP1 activity, overexpressing tara has a similar effect on the circadian period and rhythm strength as simultaneously overexpressing vri and Pdp1. Together, these results suggest that TARA modulates circadian behavior by enhancing the transcriptional activity of VRI and PDP1. |
| Mancheno-Ferris, A., Immarigeon, C., Rivero, A., Depierre, D., Schickele, N., Fosseprez, O., Chanard, N., Aughey, G., Lhoumaud, P., Anglade, J., Southall, T., Plaza, S., Payre, F., Cuvier, O., Polesello, C. (2024).. Crosstalk between chromatin and Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage. iScience, 27(1):108624 PubMed ID: 38174321
Summary: The transcription factor Shavenbaby (Svb), the only member of the OvoL family in Drosophila, controls the fate of various epithelial embryonic cells and adult stem cells. Post-translational modification of Svb produces two protein isoforms, Svb-ACT and Svb-REP, which promote adult intestinal stem cell renewal or differentiation, respectively. To define Svb mode of action, engineered cell lines were used, and an unbiased method was developed to identify Svb target genes across different contexts. Within a given cell type, Svb-ACT and Svb-REP antagonistically regulate the expression of a set of target genes, binding specific enhancers whose accessibility is constrained by chromatin landscape. Reciprocally, Svb-REP can influence local chromatin marks of active enhancers to help repressing target genes. Along the intestinal lineage, the set of Svb target genes progressively changes, together with chromatin accessibility. It is proposed that Svb-ACT-to-REP transition promotes enterocyte differentiation of intestinal stem cells through direct gene regulation and chromatin remodeling. | Bollepogu Raja, K. K., Yeung, K., Shim, Y. K., Mardon, G. (2024). Integrative genomic analyses reveal putative cell type-specific targets of the Drosophila ets transcription factor Pointed. BMC Genomics, 25(1):103 PubMed ID: 38262913
Summary: The Ets domain transcription factors direct diverse biological processes throughout all metazoans and are implicated in development as well as in tumor initiation, progression and metastasis. The Drosophila Ets transcription factor Pointed (Pnt) is the downstream effector of the Epidermal growth factor receptor (Egfr) pathway and is required for cell cycle progression, specification, and differentiation of most cell types in the larval eye disc. Despite its critical role in development, very few targets of Pnt have been reported previously. This study employed an integrated approach by combining genome-wide single cell and bulk data to identify putative cell type-specific Pnt targets. First, chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) were combined to determine the genome-wide occupancy of Pnt in late larval eye discs. Enriched regions were identified that mapped to an average of 6,941 genes, the vast majority of which are novel putative Pnt targets. Next, ChIP-seq data were integrated with two other larval eye single cell genomics datasets (scRNA-seq and snATAC-seq) to reveal 157 putative cell type-specific Pnt targets that may help mediate unique cell type responses upon Egfr-induced differentiation. Finally, these integrated data also predicts cell type-specific functional enhancers that were not reported previously. Together, this study provides a greatly expanded list of putative cell type-specific Pnt targets in the eye and is a resource for future studies that will allow mechanistic insights into complex developmental processes regulated by Egfr signaling. |
| de Almeida, B. P., Schaub, C., Pagani, M., Secchia, S., Furlong, E. E. M., Stark, A. (2023). Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo. Nature, PubMed ID: 38086418
Summary: Enhancers control gene expression and have crucial roles in development and homeostasis. However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. This study combined deep learning and transfer learning to design tissue-specific enhancers for five tissues in the Drosophila melanogaster embryo: the central nervous system, epidermis, gut, muscle and brain. Convolutional neural networks were trained using genome-wide single-cell assay for transposase-accessible chromatin with sequencing (ATAC-seq) datasets and then fine-tune the convolutional neural networks with smaller-scale data from in vivo enhancer activity assays, yielding models with 13% to 76% positive predictive value according to cross-validation. Forty synthetic enhancers (8 per tissue) were designed and experimentally assessedin vivo, of which 31 (78%) were active and 27 (68%) functioned in the target tissue (100% for central nervous system and muscle). The strategy of combining genome-wide and small-scale functional datasets by transfer learning is generally applicable and should enable the design of tissue-, cell type- and cell state-specific enhancers in any system. | Bachem, K., Li, X., Ceolin, S., Muhling, B., Horl, D., Harz, H., Leonhardt, H., Arnoult, L., Weber, S., Matarlo, B., Prud'homme, B., Gompel, N. (2024). Regulatory evolution tuning pigmentation intensity quantitatively in Drosophila. Sci Adv, 10(4):eadl2616 PubMed ID: 38266088
Summary: Quantitative variation in attributes such as color, texture, or stiffness dominates morphological diversification. It results from combinations of alleles at many Mendelian loci. This study identified an additional source of quantitative variation among species, continuous evolution in a gene regulatory region. Specifically, the modulation of wing pigmentation was examined in a group of fly species and showed that inter-species variation correlated with the quantitative expression of the pigmentation gene yellow. This variation results from an enhancer of yellow determining darkness through species-specific activity. The divergent activities were mapped between two sister species, and the changes were found to be broadly distributed along the enhancer. These results demonstrate that enhancers can act as dials fueling quantitative morphological diversification by modulating trait properties. |
Friday, September 6th - Signaling |
| Feizy, N., Leuchtenberg, S. F., Steiner, C., Wurtz, B., Fliegner, L., Huber, A. (2024). In vivo identification of Drosophila rhodopsin interaction partners by biotin proximity labeling. Scientific Reports https://www.nature.com/articles/s41598-024-52041-3
Summary: Proteins exert their function through protein-protein interactions. In Drosophila, G protein-coupled receptors like rhodopsin (Rh1) interact with a G protein to activate visual signal transduction and with arrestins to terminate activation. Also, membrane proteins like Rh1 engage in protein-protein interactions during folding within the endoplasmic reticulum, during their vesicular transport and upon removal from the cell surface and degradation. This study expressed a Rh1-TurboID fusion protein (Rh1::TbID) in Drosophila photoreceptors to identify in vivo Rh1 interaction partners by biotin proximity labeling. Rh1::TbID forms a functional rhodopsin that mediates biotinylation of arrestin 2 in conditions where arrestin 2 interacts with rhodopsin. Biotinylation was observed of Rh1::TbID and native Rh1 as well as of most visual signal transduction proteins. These findings indicate that the signaling components in the rhabdomere approach rhodopsin closely, within a range of ca. 10 nm. Furthermore, this study has detected proteins engaged in the maturation of rhodopsin and elements responsible for the trafficking of membrane proteins, resembling potential interaction partners of Rh1. Among these are chaperons of the endoplasmic reticulum, proteins involved in Clathrin-mediated endocytosis as well as previously unnoticed contributors to rhodopsin transportation, such as Rab32, Vap33, or PIP82. | Lobb-Rabe, M., Nawrocka, W. I., Zhang, R., Ashley, J., Carrillo, R. A., Ozkan, E. (2024). Neuronal wiring receptors Dprs and DIPs are GPI anchored and this modification contributes to their cell surface organization. eNeuro, PubMed ID: 38233143
Summary: The Drosophila Dpr and DIP proteins belong to the immunoglobulin superfamily of cell surface proteins (CSPs). Their hetero- and homophilic interactions have been implicated in a variety of neuronal functions, including synaptic connectivity, cell survival, and axon fasciculation. However, the signaling pathways underlying these diverse functions are unknown. To gain insight into Dpr-DIP signaling, this study sought to examine how these CSPs are associated with the membrane. Specifically, it was asked whether Dprs and DIPs are integral membrane proteins or membrane anchored through the addition of glycosylphosphatidylinositol (GPI) linkage. Most Dprs and DIPs were shown to be GPI anchored to the membrane of insect cells, and these findings were validated for some family members in vivo using Drosophila larvae, where GPI anchor cleavage results in loss of surface labeling. Additionally, GPI cleavage was shown to abrogate aggregation of insect cells expressing cognate Dpr-DIP partners. To test if the GPI anchor affects Dpr and DIP localization, it was replaced with a transmembrane domain, and perturbations of sub-cellular localization were observed on motor neurons and muscles. These data suggest that membrane anchoring of Dprs and DIPs through GPI linkage is required for localization and that Dpr-DIP intracellular signaling likely requires transmembrane co-receptors. |
| Yun, H. M., Hyun, B., Song, X., Hyun, S. (2024). Piwi expressed in Drosophila adipose tissues regulates systemic IGF signaling and growth via IGF-binding protein. Biochem Biophys Res Commun, 695:149495 PubMed ID: 38211532
Summary: Piwi and its partner, Piwi-interacting RNA (piRNA), are pivotal in suppressing the harmful effects of transposable elements (TEs) linked to genomic insertional mutagenesis. While primarily active in Drosophila's adult gonadal tissues, causing sterility in its absence, Piwi's role in post-embryonic development remains unclear. This study reveals Piwi's functional presence in the larval fat body, where it governs developmental growth through systemic insulin/insulin-like growth factor (IGF) signaling (IIS). Piwi knockdown in the fat body resulted in dysregulated TE expression, reduced developmental rate and body growth, and diminished systemic IIS activity. Notably, Piwi knockdown increased Imaginal Morphogenic Protein Late 2 (Imp-L2) expression, akin to insulin-like growth factor-binding protein 7 (IGFBP7), reducing systemic IIS and inhibiting body growth. This unveils a novel role for Piwi in larval adipose tissues, emphasizing its importance in regulating systemic IIS and overall organismal growth. | Portela, M., Mukherjee, S., Paul, S., La Marca, J. E., Parsons, L. M., Veraksa, A., Richardson, H. E. (2024). The Drosophila Tumour Suppressor Lgl and Vap33 activate the Hippo pathway by a dual mechanism. J Cell Sci, PubMed ID: 38240353
Summary: The tumour suppressor, Lethal (2) giant larvae (Lgl), is an evolutionarily conserved protein that was discovered in the vinegar fly, Drosophila, where its depletion results in tissue overgrowth and loss of cell polarity. Lgl links cell polarity and tissue growth through regulation of the Notch and the Hippo signalling pathways. Lgl regulates the Notch pathway by inhibiting V-ATPase activity via Vap33. How Lgl regulates the Hippo pathway was unclear. In this study, V-ATPase activity was shown to inhibit the Hippo pathway, whereas Vap33 acts to activate Hippo signalling. Vap33 physically and genetically interacts with the actin cytoskeletal regulators RtGEF (Pix) and Git, which also bind to Hpo, and are involved in the activation of the Hippo pathway. Additionally, this study showed that the ADP ribosylation factor Arf79F (Arf1), which is a Hpo interactor, is involved in the inhibition of the Hippo pathway. Altogether these data suggests that Lgl acts via Vap33 to activate the Hippo pathway by a dual mechanism, 1) through interaction with RtGEF/Git/Arf79F, and 2) through interaction and inhibition of the V-ATPase, thereby controlling epithelial tissue growth. |
| Lefebvre, M., Colen, J., Claussen, N., Brauns, F., Raich, M., Mitchell, N., Fruchart, M., Vitelli, V., Streichan, S. J. (2023). Learning a conserved mechanism for early neuroectoderm morphogenesis. bioRxiv, PubMed ID: 38187670
Summary: Morphogenesis is the process whereby the body of an organism develops its target shape. The morphogen BMP is known to play a conserved role across bilaterian organisms in determining the dorsoventral (DV) axis. Yet, how BMP governs the spatio-temporal dynamics of cytoskeletal proteins driving morphogenetic flow remains an open question. This study used machine learning to mine a morphodynamic atlas of Drosophila development, and construct a mathematical model capable of predicting the coupled dynamics of myosin, E-cadherin, and morphogenetic flow. Mutant analysis shows that BMP sets the initial condition of this dynamical system according to the following signaling cascade: BMP establishes DV pair-rule-gene patterns that set-up an E-cadherin gradient which in turn creates a myosin gradient in the opposite direction through mechanochemical feedbacks. Using neural tube organoids, it is argued that BMP, and the signaling cascade it triggers, prime the conserved dynamics of neuroectoderm morphogenesis from fly to humans. | Mattila, J., Viitanen, A., Fabris, G., Strutynska, T., Korzelius, J., snf Hietakangas, V. Sci Adv. (2024). Stem cell mTOR signaling directs region-specific cell fate decisions during intestinal nutrient adaptation. Science Advances,10(6):eadi2671. PubMed ID: 38335286
Summary: The adult intestine is a regionalized organ, whose size and cellular composition are adjusted in response to nutrient status. This involves dynamic regulation of intestinal stem cell (ISC) proliferation and differentiation. How nutrient signaling controls cell fate decisions to drive regional changes in cell-type composition remains unclear. This study shows that intestinal nutrient adaptation involves region-specific control of cell size, cell number, and differentiation. It was uncovered that activation of mTOR complex 1 (mTORC1) increases ISC size in a region-specific manner. mTORC1 activity promotes Delta expression to direct cell fate toward the absorptive enteroblast lineage while inhibiting secretory enteroendocrine cell differentiation. In aged flies, the ISC mTORC1 signaling is deregulated, being constitutively high and unresponsive to diet, which can be mitigated through lifelong intermittent fasting. In conclusion, mTORC1 signaling contributes to the ISC fate decision, enabling regional control of intestinal cell differentiation in response to nutrition. |
Thursday, September 5th - Vesicles and Synapse |
| Delgado, M. G., Delgado, R. (2024). Transient synaptic enhancement triggered by exogenously supplied monocarboxylate in Drosophila motoneuron synapse. Neuroscience, PubMed ID: 38220128
Summary: Current evidence suggests that glial cells provide C3 carbon sources to fuel neuronal activity; however, this notion has become challenged by biosensor studies carried out in acute brain slices or in vivo, showing that neuronal activity does not rely on the import of astrocyte-produced L-lactate. Rather, stimulated neurons become net lactate exporters, as it was also shown in Drosophila neurons, in which astrocyte-provided lactate returns as lipid droplets to be stored in glial cells. This study investigated whether exogenously supplied monocarboxylates can support Drosophila motoneuron neurotransmitter release (NTR). By assessing the excitatory post-synaptic current (EPSC) amplitude under voltage-clamp as NTR indicative, it was found that both pyruvate and L-lactate, as the only carbon sources in the synapses bathing-solution, cause a large transient NTR enhancement, which declines to reach a synaptic depression state, from which the synapses do not recover. The lipophilic dye FM1-43 pre-synaptic loading ability, however, is maintained under monocarboxylate, suggesting that SV cycling should not contribute to the synaptic depression state. The NTR recovery was reached by supplementing the monocarboxylate medium with sucrose. However, monocarboxylate addition to sucrose medium does not enhance NTR, but it does when the disaccharide concentration becomes too reduced. Thus, when pyruvate concentrations become too reduced, exogenously supplied L-lactate could be converted to pyruvate and metabolized by the neural mitochondria, triggering the NTR enhancement. | Waller, T. J., Collins, C. A. (2023). Opposing roles of Fos, Raw, and SARM1 in the regulation of axonal degeneration and synaptic structure. Frontiers in cellular neuroscience, 17:1283995 PubMed ID: 38099151
Summary: The degeneration of injured axons is driven by conserved molecules, including the sterile armadillo TIR domain-containing protein SARM1, the cJun N-terminal kinase JNK, and regulators of these proteins. These molecules are also implicated in the regulation of synapse development though the mechanistic relationship of their functions in degeneration vs. development is poorly understood. This study uncovered disparate functional relationships between SARM1 and the transmembrane protein Raw in the regulation of Wallerian degeneration and synaptic growth in motoneurons of Drosophila melanogaster. Genetic data suggest that Raw antagonizes the downstream output MAP kinase signaling mediated by Drosophila SARM1 (dSarm). This relationship is revealed by dramatic synaptic overgrowth phenotypes at the larval neuromuscular junction when motoneurons are depleted for Raw or overexpress dSarm. While Raw antagonizes the downstream output of dSarm to regulate synaptic growth, it shows an opposite functional relationship with dSarm for axonal degeneration. Loss of Raw leads to decreased levels of dSarm in axons and delayed axonal degeneration that is rescued by overexpression of dSarm, supporting a model that Raw promotes the activation of dSarm in axons. However, inhibiting Fos also decreases dSarm levels in axons but has the opposite outcome of enabling Wallerian degeneration. The combined genetic data suggest that Raw, dSarm, and Fos influence each other's functions through multiple points of regulation to control the structure of synaptic terminals and the resilience of axons to degeneration. |
| Zhang, W., Zhang, Z., Xiang, Y., Gu, D. D., Chen, J., Chen, Y., Zhai, S., Liu, Y., Jiang, T., Liu, C., He, B., Yan, M., Wang, Z., Xu, J., Cao, Y. L., Deng, B., Zeng, D., Lei, J., Zhuo, J., Lei, X., Long, Z., Jin, B., Chen, T., Li, D., Shen, Y., Hu, J., Gao, S., Liu, Q. (2024). Aurora kinase A-mediated phosphorylation triggers structural alteration of Rab1A to enhance ER complexity during mitosis. Nat Struct Mol Biol, PubMed ID: 38177680
Summary: Morphological rearrangement of the endoplasmic reticulum (ER) is critical for metazoan mitosis. Yet, how the ER is remodeled by the mitotic signaling remains unclear. This study reports that mitotic Aurora kinase A (AURKA) employs a small GTPase, Rab1A, to direct ER remodeling. During mitosis, AURKA phosphorylates Rab1A (see Drosophila Rab1) at Thr75. Structural analysis demonstrates that Thr75 phosphorylation renders Rab1A in a constantly active state by preventing interaction with GDP-dissociation inhibitor (GDI). Activated Rab1A is retained on the ER and induces the oligomerization of ER-shaping protein RTNs and REEPs, eventually triggering an increase of ER complexity. In various models, from Caenorhabditis elegans and Drosophila to mammals, inhibition of Rab1A(Thr75) phosphorylation by genetic modifications disrupts ER remodeling. Thus, this study reveals an evolutionarily conserved mechanism explaining how mitotic kinase controls ER remodeling and uncovers a critical function of Rab GTPases in metaphase. | Szenci, G., Glatz, G., Takats, S., and Juhasz, G. (2023). The Ykt6-Snap29-Syx13 SNARE complex promotes crinophagy via secretory granule fusion with Lamp1 carrier vesicles. Sci Rep. 14(1):3200. PubMed ID: 38331993
Summary: In the Drosophila larval salivary gland, developmentally programmed fusions between lysosomes and secretory granules (SGs) and their subsequent acidification promote the maturation of SGs that are secreted shortly before puparium formation. Subsequently, ongoing fusions between non-secreted SGs and lysosomes give rise to degradative crinosomes, where the superfluous secretory material is degraded. Lysosomal fusions control both the quality and quantity of SGs, however, its molecular mechanism is incompletely characterized. This study identified the R-SNARE Ykt6 as a novel regulator of crinosome formation, but not the acidification of maturing SGs. Ykt6 localizes to Lamp1+ carrier vesicles, and forms a SNARE complex with Syntaxin 13 and Snap29 to mediate fusion with SGs. These Lamp1 carriers represent a distinct vesicle population that are functionally different from canonical Arl8+, Cathepsin L+ lysosomes, which also fuse with maturing SGs but are controlled by another SNARE complex composed of Syntaxin 13, Snap29 and Vamp7. Ykt6- and Vamp7-mediated vesicle fusions also determine the fate of SGs, as loss of either of these SNAREs prevents crinosomes from acquiring endosomal PI3P. These results highlight that fusion events between SGs and different lysosome-related vesicle populations are critical for fine regulation of the maturation and crinophagic degradation of SGs. |
| Gaspar, C. J., Gomes, T., Martins, J. C., Melo, M. N., Adrain, C., Cordeiro, T. N., Domingos, P. M. (2023. Xport-A functions as a chaperone by stabilizing the first five transmembrane domains of rhodopsin-1. iScience, 26(12):108309 PubMed ID: 38025784
Summary: Rhodopsin-1 (Rh1), the main photosensitive protein of Drosophila, is a seven-transmembrane domain protein, which is inserted co-translationally in the endoplasmic reticulum (ER) membrane. Biogenesis of Rh1 occurs in the ER, where various chaperones interact with Rh1 to aid in its folding and subsequent transport from the ER to the rhabdomere, the light-sensing organelle of the photoreceptors. Xport-A has been proposed as a chaperone/transport factor for Rh1, but the exact molecular mechanism for Xport-A activity upon Rh1 is unknown. This study proposes a model where Xport-A functions as a chaperone during the biogenesis of Rh1 in the ER by stabilizing the first five transmembrane domains (TMDs) of Rh1. | Li, Y., Liu, D., Wang, H., Zhang, X., Lu, B., Li, S. (2023). The IRE1/Xbp1 axis restores ER and tissue homeostasis perturbed by excess Notch in Drosophila. Dev Biol, 507:11-19 PubMed ID: 38142805
Summary: Notch signaling controls numerous key cellular processes including cell fate determination and cell proliferation. Its malfunction has been linked to many developmental abnormalities and human disorders. Overactivation of Notch signaling is shown to be oncogenic. Retention of excess Notch protein in the endoplasmic reticulum (ER) can lead to altered Notch signaling and cell fate, but the mechanism is not well understood. This study showed that V5-tagged or untagged exogenous Notch is retained in the ER when overexpressed in fly tissues. Furthermore, Notch retention in the ER leads to robust ER enlargement and elicits a rough eye phenotype. Gain-of-function of unfolded protein response (UPR) factors IRE1 or spliced Xbp1 (Xbp1-s) alleviates Notch accumulation in the ER, restores ER morphology and ameliorates the rough eye phenotype. These results uncover a pivotal role of the IRE1/Xbp1 axis in regulating the detrimental effect of ER-localized excess Notch protein during development and tissue homeostasis. |
Wednesday, September 4th - Mammalian Homologs of Drosophila Proteins |
| Veen, K., Krylov, A., Yu, S., He, J., Boyd, P., Hyde, D. R., Mantamadiotis, T., Cheng, L. Y., Jusuf, P. R. (2023). Her6 and Prox1a are novel regulators of photoreceptor regeneration in the zebrafish retina. PLoS Genet, 19(11):e1011010 PubMed ID: 37930995
Summary: Damage to light-sensing photoreceptors (PRs) occurs in highly prevalent retinal diseases. As humans cannot regenerate new PRs, these diseases often lead to irreversible blindness. Intriguingly, animals, such as the zebrafish, can regenerate PRs efficiently and restore functional vision. Upon injury, mature Muller glia (MG) undergo reprogramming to adopt a stem cell-like state. This process is similar to cellular dedifferentiation, and results in the generation of progenitor cells, which, in turn, proliferate and differentiate to replace lost retinal neurons. This study tested whether factors involved in dedifferentiation of Drosophila CNS are implicated in the regenerative response in the zebrafish retina. It was found that hairy-related 6 (her6) (see Drosophila Hairy) negatively regulates of PR production by regulating the rate of cell divisions in the MG-derived progenitors. prospero homeobox 1a (prox1a; see Prospero) is expressed in differentiated PRs and may promote PR differentiation through phase separation. Interestingly, upon Her6 downregulation, Prox1a is precociously upregulated in the PRs, to promote PR differentiation; conversely, loss of Prox1a also induces a downregulation of Her6. Together, this study identified two novel candidates of PR regeneration that cross regulate each other; these may be exploited to promote human retinal regeneration and vision recovery. | Liu, F., Lagares, D., Choi, K. M., ..., Varelas, X., Tager, A. M., Tschumperlin, D. J. (2015). Mechanosignaling through YAP and TAZ drives fibroblast activation and fibrosis. American journal of physiology Lung cellular and molecular physiology. 308(4):L344-357 PubMed ID: 25502501
Summary: Pathological fibrosis is driven by a feedback loop in which the fibrotic extracellular matrix is both a cause and consequence of fibroblast activation. This study identified yes-associated protein (YAP) (homolog of Drosophila Yki) and transcriptional coactivator with PDZ-binding motif (TAZ), transcriptional effectors of the Hippo pathway, as key matrix stiffness-regulated coordinators of fibroblast activation and matrix synthesis. YAP and TAZ are prominently expressed in fibrotic but not healthy lung tissue, with particularly pronounced nuclear expression of TAZ in spindle-shaped fibroblastic cells. In culture, both YAP and TAZ accumulate in the nuclei of fibroblasts grown on pathologically stiff matrices but not physiologically compliant matrices. Knockdown of YAP and TAZ together in vitro attenuates key fibroblast functions, including matrix synthesis, contraction, and proliferation, and does so exclusively on pathologically stiff matrices. Profibrotic effects of YAP and TAZ operate, in part, through their transcriptional target plasminogen activator inhibitor-1, which is regulated by matrix stiffness independent of transforming growth factor-β signaling. Immortalized fibroblasts conditionally expressing active YAP or TAZ mutant proteins overcome soft matrix limitations on growth and promote fibrosis when adoptively transferred to the murine lung, demonstrating the ability of fibroblast YAP/TAZ activation to drive a profibrotic response in vivo. Together, these results identify YAP and TAZ as mechanoactivated coordinators of the matrix-driven feedback loop that amplifies and sustains fibrosis. |
| Bjarnason, G. A., Jordan, R. C., Wood, P. A., Li, Q., Lincoln, D. W., Sothern, R. B., Hrushesky, W. J., Ben-David, Y. (2001). Circadian expression of clock genes in human oral mucosa and skin: association with specific cell-cycle phases. The American journal of pathology, 158(5):1793-1801 PubMed ID: 11337377
Summary: The relative RNA expression of clock genes was studied throughout one 24-hour period in biopsies obtained from the oral mucosa and skin from eight healthy diurnally active male study participants. The human clock genes hClock, hTim, hPer1, hCry1, and hBmal1 are expressed in oral mucosa and skin, with a circadian profile consistent with that found in the suprachiasmatic nuclei and the peripheral tissues of rodents. hPer1, hCry1, and hBmal1 have a rhythmic expression, peaking early in the morning, in late afternoon, and at night, respectively, whereas hClock and hTim are not rhythmic. This is the first human study to show a circadian profile of expression for all five clock genes as documented in rodents, suggesting their functional importance in man. In concurrent oral mucosa biopsies, thymidylate synthase enzyme activity, a marker for DNA synthesis, had a circadian variation with peak activity in early afternoon, coinciding with the timing of S phase in a previous study on cell-cycle timing in human oral mucosa. The major peak in hPer1 expression occurs at the same time of day as the peak in G(1) phase in oral mucosa, suggesting a possible link between the circadian clock and the mammalian cell cycle. | Varambally, S., Dhanasekaran, S. M., Zhou, M., Barrette, T. R., Kumar-Sinha, C., Sanda, M. G., Ghosh, D., Pienta, K. J., Sewalt, R. G., Otte, A. P., Rubin, M. A., Chinnaiyan, A. M. (2002). The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature, 4 19(6907):624-629 PubMed ID: 12374981
Summary: Prostate cancer is a leading cause of cancer-related death in males and is second only to lung cancer. Although effective surgical and radiation treatments exist for clinically localized prostate cancer, metastatic prostate cancer remains essentially incurable. This study shows, through gene expression profiling, that the polycomb group protein enhancer of zeste homolog 2 (EZH2; see Drosophila Enhancer of zeste) is overexpressed in hormone-refractory, metastatic prostate cancer. Small interfering RNA (siRNA) duplexes targeted against EZH2 reduce the amounts of EZH2 protein present in prostate cells and also inhibit cell proliferation in vitro. Ectopic expression of EZH2 in prostate cells induces transcriptional repression of a specific cohort of genes. Gene silencing mediated by EZH2 requires the SET domain and is attenuated by inhibiting histone deacetylase activity. Amounts of both EZH2 messenger RNA and EZH2 protein are increased in metastatic prostate cancer; in addition, clinically localized prostate cancers that express higher concentrations of EZH2 show a poorer prognosis. Thus, dysregulated expression of EZH2 may be involved in the progression of prostate cancer, as well as being a marker that distinguishes indolent prostate cancer from those at risk of lethal progression. |
| Gessner, N. R., Peiravi, M., Zhang, F., Yimam, S., Springer, D., Harbison, S. T. (2023). A conserved role for frizzled in sleep architecture. Sleep advances : a journal of the Sleep Research Society, 4(1):zpad045 PubMed ID: 38033424
Summary: Previous studies of natural variants in Drosophila melanogaster implicated the Wnt signaling receptor frizzled in sleep. Given that the Wnt signaling pathway is highly conserved across species, it was hypothesized that frizzled class receptor 1 (Fzd1), the murine homolog of frizzled, would also have a role in sleep. Using a CRISPR transgenic approach, most of the Fzd1 coding region was removed from C57BL/6N mice. A video assay was used to measure sleep characteristics in Fzd1-deficient mice. As Wnt signaling is known to affect visuospatial memory, the impact of the deletion on learning and memory was also examined using the novel object recognition (NOR) paradigm. Fzd1-deficient mice had altered sleep compared to littermate controls. The mice did not respond differently to the NOR paradigm compared to controls but did display anxiety-like behavior. The strategy used in his research demonstrates that the study of natural variation in Drosophila sleep translates into candidate genes for sleep in vertebrate species such as the mouse. | Shen, Z., Guo, Z., Ou, G., Li, W. (2024). Inhibition of the chromatin remodeling factor NURF rescued sterility by a clinic variant of NuRD. Mol Biol Cell, 35(1):ar13 PubMed ID: 37938928
Summary: The nucleosome remodeling and deacetylase (NuRD) complex is essential for gene expression and cell fate determination, and missense mutations of NuRD caused neurodevelopmental diseases. However, the molecular pathogenesis of clinic NuRD variants is unknown. This study introduced a clinic CHD3 (L915F) variant into Caenorhabditis elegans homologue LET-418, impairing germline and vulva development and ultimately causing animal sterility. ATAC-seq and RNA-seq analyses revealed that this variant generated an abnormal open chromatin structure and disrupted the expression of developmental genes. Through genetic suppressor screens, intragenic mutations, likely renovating NuRD activity, were found to restored animal viability. It was also found that intergenic mutations in nucleosome remodeling factor NURF that counteracts NuRD rescued abnormal chromatin structure, gene expression, and animal sterility. It is proposes that two antagonistic chromatin-remodeling factors coordinate to establish the proper chromatin status and transcriptome and that inhibiting NURF may provide insights for treatment of NuRD mutation-related diseases. |
Tuesday, September 3rd - Characterization of Genes, Enzymes and Protein |
| Ziemba, P. M., Mueck, A., Gisselmann, G., Stoertkuhl, K. F. (2023). Functional expression and ligand identification of homo- and heteromeric Drosophila melanogaster CO2 receptors in the Xenopus laevis oocyte system. PLoS One, 18(12):e0295404 PubMed ID: 38157355
Summary: Carbon dioxide (CO2) is an important olfactory cue in Drosophila melanogaster and can elicit both attractive and aversive behaviors. It is detected by gustatory receptors, Gr21a and Gr63a, found in the ab1C neuron in basiconic sensilla on the third antennal segment. Volatile substances that modulate the receptors' function are of interest for pest control. While several substances block ab1C neurons or mimic the activating effect of carbon dioxide, it is not known if these substances are indeed ligands of the CO2 receptor or might act on other proteins in the receptor neuron. This study used the recombinant Xenopus laevis expression system and two-electrode voltage-clamp technology to investigate the receptor function. Application of sodium bicarbonate evokes large inward currents in oocytes co-expressing Gr21a and Gr63a. The receptors most likely form hetromultimeric complexes. Homomultimeric receptors of Gr21a or Gr63a are sufficient for receptor functionality, although oocytes gave significantly lower current responses compared to the probable heteromultimeric receptor. A screen was performed for putative blockers of the sodium bicarbonate response, and it was confirmed that some of the substances identified by spike recordings of olfactory receptor neurons, such as 1-hexanol, are also blockers in the Xenopus oocyte system. A new blocking substance, citronellol, was identified, which is related to insect repellents. Many substances that activate receptor neurons were inactive in the Xenopus oocyte system, indicating that they may not be ligands for the receptor, but may act on other proteins. However, methyl pyruvate and n-hexylamine were found to be activators of the recombinant Gr21a/Gr63a receptor. | Tan, W. J., Hawley, H. R., Wilson, S. J., Fitzsimons, H. L. (2024). Deciphering the roles of subcellular distribution and interactions involving the MEF2 binding region, the ankyrin repeat binding motif and the catalytic site of HDAC4 in Drosophila neuronal morphogenesis. BMC Biol, 22(1):2 PubMed ID: 38167120
Summary: Dysregulation of nucleocytoplasmic shuttling of histone deacetylase 4 (HDAC4) is associated with several neurodevelopmental and neurodegenerative disorders. Efficient nuclear entry is dependent on binding of the transcription factor MEF2 A series of mutants were generated for functional dissection of HDAC4 via in-depth examination of the resulting subcellular distribution and nuclear aggregation, and these were correlated with developmental phenotypes resulting from their expression in well-established models of neuronal morphogenesis of the Drosophila mushroom body and eye. Gn the mushroom body, forced sequestration of HDAC4 in the nucleus or the cytoplasm resulted in defects in axon morphogenesis. The actions of HDAC4 that resulted in impaired development were dependent on the MEF2 binding region, modulated by the ankyrin repeat binding motif, and largely independent of an intact catalytic site. In contrast, disruption to eye development was largely independent of MEF2 binding but mutation of the catalytic site significantly reduced the phenotype, indicating that HDAC4 acts in a neuronal-subtype-specific manner. This study found that the impairments to mushroom body and eye development resulting from nuclear accumulation of HDAC4 were exacerbated by mutation of the ankyrin repeat binding motif, whereas there was a differing requirement for the MEF2 binding site and an intact catalytic site. It will be of importance to determine the binding partners of HDAC4 in nuclear aggregates and in the cytoplasm of these tissues to further understand its mechanisms of action. |
| O'Haren, T., Aoki, T., Rieder, L. E. (2023). Zelda is dispensable for Drosophila melanogaster histone gene regulation. bioRxiv, PubMed ID: 38187550
Summary: To ensure that the embryo can package exponentially increasing amounts of DNA, replication-dependent histones are some of the earliest transcribed genes from the zygotic genome. However, how the histone genes are identified is not known. The pioneer factors Zelda and CLAMP collaborate at a subset of genes to regulate zygotic genome activation in Drosophila melanogaster and target early activated genes to induce transcription. CLAMP also regulates the embryonic histone genes and helps establish the histone locus body, a suite of factors that controls histone mRNA biosynthesis. The relationship between Zelda and CLAMP led to the hypothesis that Zelda helps identify histone genes for early embryonic expression. This study found that Zelda targets the histone locus early during embryogenesis, prior to histone gene expression. However, depletion of zelda in the early embryo does not affect histone mRNA levels or histone locus body formation. While surprising, these results concur with other investigations into Zelda's role in the early embryo, suggesting the earliest factors responsible for specifying the zygotic histone genes remain undiscovered. | Kitamura, D., Taniguchi, K., Nakamura, M., Igaki, T. (2024). In vivo evidence for homeostatic regulation of ribosomal protein levels in Drosophila. Cell structure and function. PubMed ID: 38199250
Summary: The ribosome is a molecular machine essential for protein synthesis, which is composed of approximately 80 different ribosomal proteins (Rps). Intracellular level of Rps is finely regulated by negative feedback mechanisms or ubiquitin-proteasome system. Using Drosophila genetics, this study shows that intracellular Rp levels are regulated by proteasomal degradation of excess Rps that are not incorporated into the ribosome. By establishing an EGFP-fused Rp gene system that can monitor endogenously expressed Rp levels, it was found that endogenously expressed EGFP-RpS20 or -RpL5 is eliminated from the cell when RpS20 or RpL5 is exogenously expressed. Notably, the level of endogenously expressed Hsp83, a housekeeping gene, was not affected by exogenous expression of Hsp83, suggesting that the strict negative regulation of excess protein is specific for intracellular Rps. Further analyses revealed that the maintenance of cellular Rp levels is not regulated at the transcriptional level but by proteasomal degradation of excess free Rps as a protein quality control mechanism. These observations provide not only the in vivo evidence for the homeostatic regulation of Rp levels but also a novel genetic strategy to study in vivo regulation of intracellular Rp levels and its role in tissue homeostasis via cell competition. |
| Stricker, A. M., Hutson, M. S., Page-McCaw, A. (2023). Piezo initiates transient production of collagen IV to repair damaged basement membranes. bioRxiv, PubMed ID: 38187749
Summary: Basement membranes are sheets of extracellular matrix separating tissue layers and providing mechanical support. Their mechanical properties are determined largely by their most abundant protein, Collagen IV (Col4). Although basement membranes are repaired after damage, little is known about how. Using the basement membrane of the adult Drosophila midgut as a model, repair was shown to be distinct from maintenance. In healthy conditions, midgut Col4 originates from the fat body, but after damage, a subpopulation of enteroblasts termed "matrix menders" transiently express Col4, and Col4 from these cells is required for repair. Activation of the mechanosensitive channel Piezo is required for matrix menders to upregulate Col4, and the signal to initiate repair is a reduction in basement membrane stiffness. These data suggests that mechanical sensitivity may be a general property of Col4-producing cells. | Hodkinson, L. J., Gross, J., Schmidt, C. A., Diaz-Saldana, P. P., Aoki, T., Rieder, L. E. (2023). Sequence reliance of a Drosophila context-dependent transcription factor. bioRxiv, PubMed ID: 38106168
Summary: Despite binding similar cis elements in multiple locations, a single transcription factor often performs context-dependent functions at different loci. How factors integrate cis sequence and genomic context is still poorly understood and has implications for off-target effects in genetic engineering. The Drosophila context-dependent transcription factor CLAMP targets similar GA-rich cis elements on the X-chromosome and at the histone gene locus but recruits very different, loci-specific factors. CLAMP was found to leverages information from both cis element and local sequence to perform context-specific functions. These observations imply the importance of other cues, including protein-protein interactions and the presence of additional cofactors. |
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