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| ARCHIVE | Thursday, January 30th - Tumors and Growth |
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December 2024 November 2024 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 | Waghmare, I., Gangwani, K., Rai, A., Singh, A., Kango-Singh, M. (2024). A Tumor-Specific Molecular Network Promotes Tumor Growth in Drosophila by Enforcing a Jun N-Terminal Kinase-Yorkie Feedforward Loop. Cancers, 16(9) PubMed ID: 38730720
Summary: Cancer cells expand rapidly in response to altered intercellular and signaling interactions to achieve the hallmarks of cancer. Impaired cell polarity combined with activated oncogenes is known to promote several hallmarks of cancer, e.g., activating invasion by increased activity of Jun N-terminal kinase (JNK) and sustained proliferative signaling by increased activity of Hippo effector Yorkie (Yki). Thus, JNK, Yki, and their downstream transcription factors have emerged as synergistic drivers of tumor growth through pro-tumor signaling and intercellular interactions like cell competition. However, little is known about the signals that converge onto JNK and Yki in tumor cells and enable tumor cells to achieve the hallmarks of cancer. Using mosaic models of cooperative oncogenesis (Ras(V12),scrib(-)) in Drosophila, this study showed that Ras(V12),scrib(-) tumor cells grow through the activation of a previously unidentified network comprising Wingless (Wg), Dronc, JNK, and Yki. Ras(V12),scrib(-) cells show increased Wg, Dronc, JNK, and Yki signaling, and all these signals are required for the growth of Ras(V12),scrib(-) tumors. Wg and Dronc converge onto a JNK-Yki self-reinforcing positive feedback signal-amplification loop that promotes tumor growth. The Wg-Dronc-Yki-JNK molecular network is specifically activated in polarity-impaired tumor cells and not in normal cells, in which apical-basal polarity remains intact. These findings suggest that the identification of molecular networks may provide significant insights into the key biologically meaningful changes in signaling pathways and paradoxical signals that promote tumorigenesis. | Akiki, P., Delamotte, P., Poidevin, M., van Dijk, E. L., Petit, A. J. R., Le Rouzic, A., Mery, F., Marion-Poll, F., Montagne, J. (2024). Male manipulation impinges on social-dependent tumor suppression in Drosophila melanogaster females. Sci Rep, 14(1):6411 PubMed ID: 38494531
Summary: Physiological status can influence social behavior, which in turn can affect physiology and health. Previous, work showed that tumor growth in Drosophila virgin females depends on the social context, but did not investigate the underlying physiological mechanisms.This study sought to characterize the signal perceived between tumorous flies, ultimately discovering that the tumor suppressive effect varies depending on reproductive status. Firstly, the tumor suppressive effect was neither dependent on remnant pheromone-like products nor on the microbiota. Transcriptome analysis of the heads of these tumorous flies reveals social-dependent gene-expression changes related to nervous-system activity, suggesting that a cognitive-like relay might mediate the tumor suppressive effect. The transcriptome also reveals changes in the expression of genes related to mating behavior. Surprisingly, this social-dependent tumor-suppressive effect is lost in fertilized females. After mating, Drosophila females change their behavior-favoring offspring survival-in response to peptides transferred via the male ejaculate, a phenomenon called "male manipulation". Remarkably, the social-dependent tumor suppressive effect is restored in females mated by sex-peptide deficient males. Since male manipulation has likely been selected to favor male gene transmission, these findings indicate that this evolutionary trait impedes social-dependent tumor growth slowdown. |
| Molnar, C., Heinen, J. P., Reina, J., Llamazares, S., Palumbo, E., Pollarolo, G., Gonzalez, C. (2024). TrxT and dhd are dispensable for Drosophila brain development but essential for l(3)mbt brain tumour growth. EMBO reports, 25(7):2842-2860 PubMed ID: 38750349
Summary: Expression of the Drosophila cancer-germline (CG), X-linked, head-to-head gene pair TrxT and dhd is normally germline-specific but becomes upregulated in brain tumours caused by mutation in l(3)mbt. This study showed that TrxT and dhd play a major synergistic role in the emergence of l(3)mbt tumour-linked transcriptomic signatures and tumour development, which is remarkable, taking into account that these two genes are never expressed together under normal conditions. TrxT, but not dhd, is crucial for the growth of l(3)mbt allografts, hence suggesting that the initial stages of tumour development and long-term tumour growth may depend on different molecular pathways. In humans, head-to-head inverted gene pairs are abundant among CG genes that map to the X chromosome. These results identify a first example of an X-linked, head-to-head CG gene pair in Drosophila, underpinning the potential of such CG genes, dispensable for normal development and homoeostasis of somatic tissue, as targets to curtail malignant growth with minimal impact on overall health. | Rawal, C. C., Loubiere, V., Butova, N. L., Garcia, J., Parreno, V., Martinez, A. M., Cavalli, G., Chiolo, I. (2024). Sustained inactivation of the Polycomb PRC1 complex induces DNA repair defects and genomic instability in epigenetic tumors. Research square, PubMed ID: 38746379
Summary: Cancer initiation and progression are typically associated with the accumulation of driver mutations and genomic instability. However, recent studies demonstrated that cancers can also be purely initiated by epigenetic alterations, without driver mutations. Specifically, a 24-hours transient down-regulation of polyhomeotic (ph-KD), a core component of the Polycomb complex PRC1, is sufficient to drive epigenetically initiated cancers (EICs) in Drosophila, which are proficient in DNA repair and are characterized by a stable genome. Whether genomic instability eventually occurs when PRC1 down-regulation is performed for extended periods of time remains unclear. This study shows that prolonged depletion of a PRC1 component, which mimics cancer initiating events, results in broad dysregulation of DNA replication and repair genes, along with the accumulation of DNA breaks, defective repair, and widespread genomic instability in the cancer tissue. A broad mis-regulation of H2AK118 ubiquitylation and to a lesser extent of H3K27 trimethylation also occurs, and might contribute to these phenotypes. Together, this study supports a model where DNA repair and replication defects amplify the tumorigenic transformation epigenetically induced by PRC1 loss, resulting in genomic instability and cancer progression. |
| Datta, I., Bangi, E. (2024). Senescent cells and macrophages cooperate through a multi-kinase signaling network to promote intestinal transformation in Drosophila. Dev Cell, 59(5):566-578 PubMed ID: 38309266
Summary: Cellular senescence is a conserved biological process that plays a crucial and context-dependent role in cancer. The highly heterogeneous and dynamic nature of senescent cells and their small numbers in tissues make in vivo mechanistic studies of senescence challenging. As a result, how multiple senescence-inducing signals are integrated in vivo to drive senescence in only a small number of cells is unclear. Thiw study identified cells that exhibit multiple features of senescence in a Drosophila model of intestinal transformation, which emerge in response to concurrent activation of AKT, JNK, and DNA damage signaling within transformed tissue. Eliminating senescent cells, genetically or by treatment with senolytic compounds, reduces overgrowth and improves survival. Senescent cells promote tumorigenesis by recruiting Drosophila macrophages to the transformed tissue, which results in non-autonomous activation of JNK signaling. These findings identify senescent cell-macrophage interactions as an important driver of epithelial transformation. | Kwok, S. H., Liu, Y., Bilder, D., Kim, J. (2024). Paraneoplastic renal dysfunction in fly cancer models driven by inflammatory activation of stem cells. bioRxiv, PubMed ID: 38585959
Summary: Tumors can induce systemic disturbances in distant organs, leading to physiological changes that enhance host morbidity. In Drosophila cancer models, tumors have been known for decades to cause hypervolemic 'bloating' of the abdominal cavity. This study used allograft and transgenic tumors to show that hosts display fluid retention associated with autonomously defective secretory capacity of fly renal tubules, which function analogous to those of the human kidney. Excretion from these organs is blocked by abnormal cells that originate from inappropriate activation of normally quiescent renal stem cells (RSCs). Blockage is initiated by IL-6-like oncokines that perturb renal water-transporting cells, and trigger a damage response in RSCs that proceeds pathologically. Thus, a chronic inflammatory state produced by the tumor causes paraneoplastic fluid dysregulation by altering cellular homeostasis of host renal units. |
Tuesday, January 29th - Synapse and Vesicles |
| Hines, A. D., Kewin, A. B., Van De Poll, M. N., Anggono, V., Bademosi, A. T., van Swinderen, B. (2024). Synapse-Specific Trapping of SNARE Machinery Proteins in the Anesthetized Drosophila Brain. J Neurosci, 44(24) PubMed ID: 38749704
Summary: General Anesthetics disrupt brain network dynamics through multiple pathways, in part through postsynaptic potentiation of inhibitory ion channels as well as presynaptic inhibition of neuroexocytosis. Common clinical general anesthetic drugs, such as propofol and isoflurane, have been shown to interact and interfere with core components of the exocytic release machinery to cause impaired neurotransmitter release. Recent studies however suggest that these drugs do not affect all synapse subtypes equally. This study investigated the role of the presynaptic release machinery in multiple neurotransmitter systems under isoflurane general anesthesia in the adult female Drosophila brain using live-cell super-resolution microscopy and optogenetic readouts of exocytosis and neural excitability. Neurotransmitter-specific mushroom body output neurons were activated, and presynaptic function was imaged under isoflurane anesthesia. Isoflurane was found to impair synaptic release and presynaptic protein dynamics in excitatory cholinergic synapses. In contrast, isoflurane had little to no effect on inhibitory GABAergic or glutamatergic synapses. These results present a distinct inhibitory mechanism for general anesthesia, whereby neuroexocytosis is selectively impaired at excitatory synapses, while inhibitory synapses remain functional. This suggests a presynaptic inhibitory mechanism that complements the other inhibitory effects of these drugs. | Dresselhaus, E. C., Harris, K. P., Blanchette, C. R., Koles, K., Del Signore, S. J., Pescosolido, M. F., Ermanoska, B., Rozencwaig, M., Soslowsky, R. C., Parisi, M. J., Stewart, B. A., Mosca, T. J., Rodal, A. A. (2024). ESCRT disruption provides evidence against transsynaptic signaling functions for extracellular vesicles. bioRxiv, PubMed ID: 38746182
Summary: Extracellular vesicles (EVs) are released by many cell types including neurons, carrying cargoes involved in signaling and disease. It is unclear whether EVs promote intercellular signaling or serve primarily to dispose of unwanted materials.This study shows that loss of multivesicular endosome-generating EESCRT (endosomal sorting complex required for transport) machinery disrupts release of EV cargoes from Drosophila motor neurons. Surprisingly, ESCRT depletion does not affect the signaling activities of the EV cargo A HREF="http://flybase.org/reports/FBgn0028400.htm">Synaptotagmin-4 (Syt4)> and disrupts only some signaling activities of the EV cargo Evenness Interrupted (Evi). Thus, these cargoes may not require intercellular transfer via EVs, and instead may be conventionally secreted or function cell autonomously in the neuron. EVs are phagocytosed by glia and muscles, and ESCRT disruption causes compensatory autophagy in presynaptic neurons, suggesting that EVs are one of several redundant mechanisms to remove cargoes from synapses. These results suggest that synaptic EV release serves primarily as a proteostatic mechanism for certain cargoes. |
| DePew, A. T., Bruckner, J. J., O'Connor-Giles, K. M., Mosca, T. J. (2024). Neuronal LRP4 directs the development, maturation and cytoskeletal organization of Drosophila peripheral synapses. Development, 151(11) PubMed ID: 38738619
Summary: Synaptic development requires multiple signaling pathways to ensure successful connections. Transmembrane receptors are optimally positioned to connect the synapse and the rest of the neuron, often acting as synaptic organizers to synchronize downstream events. One such organizer, the LDL receptor-related protein LRP4, is a cell surface receptor that has been most well-studied postsynaptically at mammalian neuromuscular junctions. Recent work, however, identified emerging roles, but how LRP4 acts as a presynaptic organizer and the downstream mechanisms of LRP4 are not well understood. This study shows that LRP4 functions presynaptically at Drosophila neuromuscular synapses, acting in motoneurons to instruct pre- and postsynaptic development. Loss of presynaptic LRP4 results in multiple defects, impairing active zone organization, synapse growth, physiological function, microtubule organization, synaptic ultrastructure and synapse maturation. LRP4 was further demonstrated to promotes most aspects of presynaptic development via a downstream SR-protein kinase, SRPK79D. These data demonstrate a function for presynaptic LRP4 as a peripheral synaptic organizer, highlight a downstream mechanism conserved with its CNS function in Drosophila, and underscore previously unappreciated but important developmental roles for LRP4 in cytoskeletal organization, synapse maturation and active zone organization. | Guo, X., Mutch, M., Torres, A. Y., Nano, M., Rauth, N., Harwood, J., McDonald, D., Chen, Z., Montell, C., Dai, W., Montell, D. J. (2024). The Zn(2+) transporter ZIP7 enhances endoplasmic-reticulum-associated protein degradation and prevents neurodegeneration in Drosophila. Dev Cell, 59(13):1655-1667. PubMed ID: 38670102
Summary: Proteotoxic stress drives numerous degenerative diseases. Cells initially adapt to misfolded proteins by activating the unfolded protein response (UPR), including endoplasmic-reticulum-associated protein degradation (ERAD). However, persistent stress triggers apoptosis. Enhancing ERAD is a promising therapeutic approach for protein misfolding diseases. The ER-localized Zn(2+) transporter ZIP7 is conserved from plants to humans and required for intestinal self-renewal, Notch signaling, cell motility, and survival. However, a unifying mechanism underlying these diverse phenotypes was unknown. In studying Drosophila border cell migration, ZIP7-mediated Zn(2+) transport was discovered to enhance the obligatory deubiquitination of proteins by the Rpn11 Zn(2+) metalloproteinase in the proteasome lid. In human cells, ZIP7 and Zn(2+) are limiting for deubiquitination. In a Drosophila model of neurodegeneration caused by misfolded rhodopsin (Rh1), ZIP7 overexpression degrades misfolded Rh1 and rescues photoreceptor viability and fly vision. Thus, ZIP7-mediated Zn(2+) transport is a previously unknown, rate-limiting step for ERAD in vivo with therapeutic potential in protein misfolding diseases. |
| Kim, Y. D., Park, H. G., Song, S., Kim, J., Lee, B. J., Broadie, K., Lee, S. (2024). Presynaptic structural and functional plasticity are coupled by convergent Rap1 signaling. J Cell Biol, 223(7) PubMed ID: 38748250
Summary: Dynamic presynaptic actin remodeling drives structural and functional plasticity at synapses, but the underlying mechanisms remain largely unknown. Previous work has shown that actin regulation via Rac1 guanine exchange factor (GEF) Vav signaling restrains synaptic growth via bone morphogenetic protein (BMP)-induced receptor macropinocytosis and mediates synaptic potentiation via mobilization of reserve pool vesicles in presynaptic boutons. This study found that Gef26/PDZ-GEF and small GTPase Rap1 signaling couples the BMP-induced activation of Abelson kinase to this Vav-mediated macropinocytosis. Moreover, adenylate cyclase Rrutabaga (Rut) signaling via exchange protein activated by cAMP (Epac) drives the mobilization of reserve pool vesicles during post-tetanic potentiation (PTP). Rap1 couples activation of Rut-cAMP-Epac signaling to Vav-mediated synaptic potentiation. These findings indicate that Rap1 acts as an essential, convergent node for Abelson kinase and cAMP signaling to mediate BMP-induced structural plasticity and activity-induced functional plasticity via Vav-dependent regulation of the presynaptic actin cytoskeleton. | Soltani, S., Webb, S. M., Kroll, T., King-Jones, K. (2024). Drosophila Evi5 is a critical regulator of intracellular iron transport via transferrin and ferritin interactions. Nat Commun, 15(1):4045 PubMed ID: 38744835
Summary: Vesicular transport is essential for delivering cargo to intracellular destinations. Evi5 is a Rab11-GTPase-activating protein involved in endosome recycling. In humans, Evi5 is a high-risk locus for multiple sclerosis, a debilitating disease that also presents with excess iron in the CNS. In insects, the prothoracic gland (PG) requires entry of extracellular iron to synthesize steroidogenic enzyme cofactors. The mechanism of peripheral iron uptake in insect cells remains controversial. This study shows that Evi5-depletion in the Drosophila PG affected vesicle morphology and density, blocked endosome recycling and impaired trafficking of transferrin-1, thus disrupting heme synthesis due to reduced cellular iron concentrations. Wferritin was shown to deliver iron to the PG as well, and interacts physically with Evi5. Further, ferritin-injection rescued developmental delays associated with Evi5-depletion. To summarize, these findings show that Evi5 is critical for intracellular iron trafficking via transferrin-1 and ferritin, and implicate altered iron homeostasis in the etiology of multiple sclerosis. |
Monday, January 28th - Chromatin |
| Crain, A. T., Nevil, M., Leatham-Jensen, M. P., Reeves, K. B., Matera, A. G., McKay, D. J., Duronio, R. J. (2024). Redesigning the Drosophila histone gene cluster: An improved genetic platform for spatiotemporal manipulation of histone function. bioRxiv, PubMed ID: 38712307
Summary: Mutating replication-dependent (RD) histone genes is an important tool for understanding chromatin-based epigenetic regulation. Deploying this tool in metazoan models is particularly challenging because RD histones in these organisms are typically encoded by many genes, often located at multiple loci. Such RD histone gene arrangements make the ability to generate homogenous histone mutant genotypes by site-specific gene editing quite difficult. Drosophila melanogaster provides a solution to this problem because the RD histone genes are organized into a single large tandem array that can be deleted and replaced with transgenes containing mutant histone genes. In the last ∼15 years several different RD histone gene replacement platforms have been developed using this simple strategy. However, each platform contains weaknesses that preclude full use of the powerful developmental genetic capabilities available to Drosophila researchers. This study describes the development of a newly engineered platform that rectifies many of these weaknesses. CRISPR was used to precisely delete the RD histone gene array (HisC), replacing it with a multifunctional cassette that permits site-specific insertion of either one or two synthetic gene arrays using selectable markers. This cassette was designed with the ability to selectively delete each of the integrated gene arrays in specific tissues using site-specific recombinases. A method for rapidly synthesizing histone gene arrays of any genotype using Golden Gate cloning technologies. These improvements facilitate generation of histone mutant cells in various tissues at different stages of Drosophila development and provide an opportunity to apply forward genetic strategies to interrogate chromatin structure and gene regulation. | Afanasyev, A. Y., Kim, Y., Tolokh, I. S., Sharakhov, I. V., Onufriev, A. V. (2024). The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies. Epigenetics & chromatin, 17(1):13 PubMed ID: 38705995
Summary: Multiple studies have demonstrated a negative correlation between gene expression and positioning of genes at the nuclear envelope (NE) lined by nuclear lamina, but the exact relationship remains unclear, especially in light of the highly stochastic, transient nature of the gene association with the NE. This study asked whether there is a causal, systematic, genome-wide relationship between the expression levels of the groups of genes in topologically associating domains (TADs) of Drosophila nuclei and the probabilities of TADs to be found at the NE. To investigate the nature of this possible relationship, a coarse-grained dynamic model of the entire Drosophila nucleus was combined with genome-wide gene expression data; the TAD averaged transcription levels of genes were analyzed against the probabilities of individual TADs to be in contact with the NE in the control and lamins-depleted nuclei. These findings demonstrate that, within the statistical error margin, the stochastic positioning of Drosophila melanogaster TADs at the NE does not, by itself, systematically affect the mean level of gene expression in these TADs, while the expected negative correlation is confirmed. The correlation is weak and disappears completely for TADs not containing lamina-associated domains (LADs) or TADs containing LADs, considered separately. Verifiable hypotheses regarding the underlying mechanism for the presence of the correlation without causality are discussed. These include the possibility that the epigenetic marks and affinity to the NE of a TAD are determined by various non-mutually exclusive mechanisms and remain relatively stable during interphase. At the level of TADs, the probability of chromatin being in contact with the nuclear envelope has no systematic, causal effect on the transcription level in Drosophila. The conclusion is reached by combining model-derived time-evolution of TAD locations within the nucleus with their experimental gene expression levels. |
| Lou, Y., Wu, L., Cai, W., Deng, H., Sang, R., Xie, S., Xu, X., Yuan, X., Wu, C., Xu, M., Ge, W., Xi, Y., Yang, X. (2024). The FAcilitates Chromatin Transcription complex regulates the ratio of glycolysis to oxidative phosphorylation in neural stem cells. J Mol Cell Biol, PubMed ID: 38719542
Summary: Defects in the FAcilitates Chromatin Transcription (FACT) complex, a histone chaperone composed of SSRP1 and SUPT16H, are implicated in intellectual disability. This study reveals that the FACT complex promotes glycolysis and sustains the correct cell fate of neural stem cells/neuroblasts in the Drosophila 3rd instar larval central brain. This study shows that the FACT complex binds to the promoter region of the estrogen-related receptor (ERR) gene and positively regulates ERR expression. ERR is known to act as an aerobic glycolytic switch by upregulating the enzymes required for glycolysis. Dysfunction of the FACT complex leads to the downregulation of ERR transcription, resulting in a decreased ratio of glycolysis to oxidative phosphorylation (G/O) in neuroblasts. Consequently, neuroblasts exhibit smaller cell sizes, lower proliferation potential, and altered cell fates. Overexpression of ERR or suppression of mitochondrial oxidative phosphorylation in neuroblasts increases the relative G/O ratio and rescues defective phenotypes caused by dysfunction of the FACT complex. Thus, the G/O ratio, mediated by the FACT complex, plays a crucial role in neuroblast cell fate maintenance. This study may shed light on the mechanism by which mutations in the FACT complex lead to intellectual disability in humans. | Bamgbose, G., Bordet, G., Lodhi, N., Tulin, A. (2024). Mono-methylated histones control PARP-1 in chromatin and transcription. Elife, 13 PubMed ID: 38690995
Summary: PARP-1 is central to transcriptional regulation under both normal and stress conditions, with the governing mechanisms yet to be fully understood. Biochemical and ChIP-seq-based analyses showed that PARP-1 binds specifically to active histone marks, particularly H4K20me1. This study found that H4K20me1 plays a critical role in facilitating PARP-1 binding and the regulation of PARP-1-dependent loci during both development and heat shock stress. The sole H4K20 mono-methylase, pr-set7, and parp-1 Drosophila mutants undergo developmental arrest. RNA-seq analysis showed an absolute correlation between PR-SET7- and PARP-1-dependent loci expression, confirming co-regulation during developmental phases. PARP-1 and PR-SET7 are both essential for activating hsp70 and other heat shock genes during heat stress, with a notable increase of H4K20me1 at their gene body. Mutating pr-set7 disrupts monomethylation of H4K20 along heat shock loci and abolish PARP-1 binding there. These data strongly suggest that H4 monomethylation is a key triggering point in PARP-1 dependent processes in chromatin. |
| Gurgo, J., Walter, J. C., Fiche, J. B., Houbron, C., Schaeffer, M., Cavalli, G., Bantignies, F., Nollmann, M. (2024). Multiplexed chromatin imaging reveals predominantly pairwise long-range coordination between Drosophila Polycomb genes. Cell Rep, 43(5):114167 PubMed ID: 38691452
Summary: Polycomb (Pc) group proteins are transcriptional regulators with key roles in development, cell identity, and differentiation. Pc-bound chromatin regions form repressive domains that interact in 3D to assemble repressive nuclear compartments. This study used multiplexed chromatin imaging to investigate whether Pc compartments involve the clustering of multiple Pc domains during Drosophila development. Notably, 3D proximity between Pc targets is rare and involves predominantly pairwise interactions. These 3D proximities are particularly enhanced in segments where Pc genes are co-repressed. In addition, segment-specific expression of Hox Pc targets leads to their spatial segregation from Pc-repressed genes. Finally, non-Hox Pc targets are more proximal in regions where they are co-expressed. These results indicate that long-range Pc interactions are temporally and spatially regulated during differentiation and development but do not induce frequent clustering of multiple distant Pc genes. | Melnikova, L. S., Molodina, V. V., Georgiev, P. G., Golovnin, A. K. (2024). Impact of Interactions between Su(Hw)-Dependent Insulators on the Transvection Effect in Drosophila melanogaster. Doklady Biochemistry and biophysics, 517(1):127-133 PubMed ID: 38744735
Summary: Transvection is a phenomenon of interallelic communication in which enhancers can activate a specific promoter located on a homologous chromosome. Insulators play a significant role in ensuring functional interactions between enhancers and promoters. This study created a model where two or three copies of the insulator are located next to enhancers and promoters localized on homologous chromosomes. Using the Su(Hw) insulator as a model, this study showed that the functional interaction between a pair of insulators promotes enhancer-promoter trans-interactions. The interaction between the three insulators, on the contrary, can lead to the formation of chromatin loops that sterically hinder the full enhancer-promoter interaction. The results of the work suggest the participation of insulators in the regulation of homologous chromosome pairing and in communication between distant genomic loci. |
Friday, January 24th - Immune Respoonse |
| McMullen, E., Strych, L., Chodakova, L., Krebs, A., Dolezal, T. (2024). JAK/STAT mediated insulin resistance in muscles is essential for effective immune response. Cell Commun Signal, 22(1):203 PubMed ID: 38566182
Summary: The metabolically demanding nature of immune response requires nutrients to be preferentially directed towards the immune system at the expense of peripheral tissues. The mechanisms by which this metabolic reprograming occurs was studied using the parasitoid infection of Drosophila larvae. To overcome such an immune challenge hemocytes differentiate into lamellocytes, which encapsulate and melanize the parasitoid egg. Hemocytes acquire the energy for this process by expressing JAK/STAT ligands upd2 and upd3, which activates JAK/STAT signaling in muscles and redirects carbohydrates away from muscles in favor of immune cells. Immune response of Drosophila larvae was induced by parasitoid wasp infestation. Carbohydrate levels, larval locomotion and gene expression of key proteins were compared between control and infected animals. Efficacy of lamellocyte production and resistance to wasp infection was observed for RNAi and mutant animals. Absence of Upd/JAK/STAT signaling leads to an impaired immune response and increased mortality. This study demonstrates how JAK/STAT signaling in muscles leads to suppression of insulin signaling through activation of ImpL2, the inhibitor of Drosophila insulin like peptides. These findings reveal cross-talk between immune cells and muscles mediates a metabolic shift, redirecting carbohydrates towards immune cells. It is emphasize the crucial function of muscles during immune response and show the benefits of insulin resistance as an adaptive mechanism that is necessary for survival. | Chen, D., Shi, C., Xu, W., Rong, Q., Wu, Q. (2024). Regulation of phase separation and antiviral activity of Cactin by glycolytic enzyme PGK via phosphorylation in Drosophila. mBio, 15(4):e0137823 PubMed ID: 38446061
Summary: Liquid-liquid phase separation (LLPS) plays a crucial role in various biological processes in eukaryotic organisms, including immune responses in mammals. However, the specific function of LLPS in immune responses in Drosophila melanogaster remains poorly understood. Cactin, a highly conserved protein in eukaryotes, is involved in a non-canonical signaling pathway associated with Nuclear factor-κB (NF-κB)-related pathways in Drosophila. This study investigated the role of Cactin in LLPS and its implications for immune response modulation. Cactin was found to undergoes LLPS, forming droplet-like particles, primarily mediated by its intrinsically disordered region (IDR). Utilizing immunoprecipitation and mass spectrometry analysis, this study identified two phosphorylation sites at serine residues 99 and 104 within the IDR1 domain of Cactin. Co-immunoprecipitation and mass spectrometry further revealed phosphoglycerate kinase (PGK) as a Cactin-interacting protein responsible for regulating its phosphorylation. Phosphorylation of Cactin by PGK induced a transition from stable aggregates to dynamic liquid droplets, enhancing its ability to interact with other components in the cellular environment. Overexpression of PGK inhibited Drosophila C virus (DCV) replication, while PGK knockdown increased replication. DCV infection also increased Cactin phosphorylation. Phosphorylation was found to enhance the antiviral ability of Cactin by promoting liquid-phase droplet formation. These findings demonstrate the role of Cactin-phase separation in regulating DCV replication and highlight the modulation of its antiviral function through phosphorylation, providing insights into the interplay between LLPS and antiviral defense mechanisms. |
| Kazek, M., Chodakova, L., Lehr, K., Strych, L., Nedbalova, P., McMullen, E., Bajgar, A., Opekar, S., Simek, P., Moos, M., Dolezal, T. (2024). Glucose and trehalose metabolism through the cyclic pentose phosphate pathway shapes pathogen resistance and host protection in Drosophila. PLoS Biol, 22(5):e3002299 PubMed ID: 38713712
Summary: Activation of immune cells requires the remodeling of cell metabolism in order to support immune function. These metabolic changes were studied through the infection of Drosophila larvae by parasitoid wasp. The parasitoid egg is neutralized by differentiating lamellocytes, which encapsulate the egg. A melanization cascade is initiated, producing toxic molecules to destroy the egg while the capsule also protects the host from the toxic reaction. This study combined transcriptomics and metabolomics, including 13C-labeled glucose and trehalose tracing, as well as genetic manipulation of sugar metabolism to study changes in metabolism, specifically in Drosophila hemocytes. Hemocytes were found to increase the expression of several carbohydrate transporters and accordingly uptake more sugar during infection. These carbohydrates are metabolized by increased glycolysis, associated with lactate production, and cyclic pentose phosphate pathway (PPP), in which glucose-6-phosphate is re-oxidized to maximize NADPH yield. Oxidative PPP is required for lamellocyte differentiation and resistance, as is systemic trehalose metabolism. In addition, fully differentiated lamellocytes use a cytoplasmic form of trehalase to cleave trehalose to glucose and fuel cyclic PPP. Intracellular trehalose metabolism is not required for lamellocyte differentiation, but its down-regulation elevates levels of reactive oxygen species, associated with increased resistance and reduced fitness. These results suggest that sugar metabolism, and specifically cyclic PPP, within immune cells is important not only to fight infection but also to protect the host from its own immune response and for ensuring fitness of the survivor. | Wang, Z., Lin, X., Shi, W., Cao, C. (2024). Nicotinic Acetylcholine Receptor Alpha6 Contributes to Antiviral Immunity via IMD Pathway in Drosophila melanogaster. Viruses, 16(4) PubMed ID: 38675904
Summary: Currently, insecticides that target nicotinic acetylcholine receptors (nAChR) are widely used. Studies on the sublethal effects of insecticides have found that they can affect the amount of virus in insects. The mechanism by which insecticides affect insect virus load remain unclear. This study shows that nAChR targeting insecticide can affect viral replication through the immune deficiency (IMD) pathway. A low dose of spinosad (6.8 ng/mL), acting as an antagonist to Drosophila melanogaster nicotinic acetylcholine receptor α6 (Dα6), significantly elevates Drosophila melanogaster sigmavirus (DMelSV) virus titers in adults of Drosophila melanogaster. Conversely, a high dose of spinosad (50 ng/mL), acting as an agonist to Dα6, substantially decreases viral load. This bidirectional regulation of virus levels is absent in Dα6-knockout flies, signifying the specificity of spinosad's action through Dα6. Furthermore, the knockdown of Dα6 results in decreased expression of genes in the IMD pathway, including dredd, imd, relish, and downstream antimicrobial peptide genes AttA and AttB, indicating a reduced innate immune response. Subsequent investigations reveal no significant difference in viral titers between relish mutant flies and Dα6-relish double mutants, suggesting that the IMD pathway's role in antiviral defense is dependent on Dα6. Collectively, these findings shed light on the intricate interplay between nAChR signaling and the IMD pathway in mediating antiviral immunity, highlighting the potential for nAChR-targeting compounds to inadvertently influence viral dynamics in insect hosts. This knowledge may inform the development of integrated pest management strategies that consider the broader ecological impact of insecticide use. |
| Fioriti, F., Rifflet, A., Gomperts Boneca, I., Zugasti, O., Royet, J. (2024). Bacterial peptidoglycan serves as a critical modulator of the gut-immune-brain axis in Drosophila. Brain, behavior, and immunity, 119:878-897 PubMed ID: 38710338
Summary: Metabolites and compounds derived from gut-associated bacteria can modulate numerous physiological processes in the host, including immunity and behavior. Using a model of oral bacterial infection, previous work demonstrated that gut-derived peptidoglycan (PGN), an essential constituent of the bacterial cell envelope, influences female fruit fly egg-laying behavior by activating the NF-κB cascade in a subset of brain neurons. These findings underscore PGN as a potential mediator of communication between gut bacteria and the brain in Drosophila, prompting further investigation into its impact on all brain cells. Through high-resolution mass spectrometry, this study shows that PGN fragments produced by gut bacteria can rapidly reach the central nervous system. In Addition, by employing a combination of whole-genome transcriptome analyses, comprehensive genetic assays, and reporter gene systems, it was revealed that gut bacterial infection triggers a PGN dose-dependent NF-κB immune response in perineurial glia, forming the continuous outer cell layer of the blood-brain barrier. Furthermore, it was demonstrated that persistent PGN-dependent NF-κB activation in perineurial glial cells correlates with a reduction in lifespan and early neurological decline. Overall, these findings establish gut-derived PGN as a critical mediator of the gut-immune-brain axis in Drosophila. | Wang, J., Gu, J., Yi, J., Li, J., Li, W., Zhai, Z. (2024). High-fat diets induce inflammatory IMD/NFκB signaling via gut microbiota remodeling in Drosophila. Frontiers in cellular and infection microbiology, 14:1347716 PubMed ID: 38716198
Summary: High-fat diets (HFDs), a prevailing daily dietary style worldwide, induce chronic low-grade inflammation in the central nervous system and peripheral tissues, promoting a variety of diseases including pathologies associated with neuroinflammation. However, the mechanisms linking HFDs to inflammation are not entirely clear. Using a Drosophila HFD model, this study explored the mechanism of HFD-induced inflammation in remote tissues. HFDs were found to activate the IMD/NFκB immune pathway in the head through remodeling of the commensal gut bacteria. Removal of gut microbiota abolished such HFD-induced remote inflammatory response. Further experiments revealed that HFDs significantly increased the abundance of Acetobacter malorum in the gut, and the re-association of this bacterium was sufficient to elicit inflammatory response in remote tissues. Mechanistically, Acetobacter malorum produced a greater amount of peptidoglycan (PGN), a well-defined microbial molecular pattern that enters the circulation and remotely activates an inflammatory response. These results thus show that HFDs trigger inflammation mediated by a bacterial molecular pattern that elicits host immune response. |
Thursday, January 23rd - Gonads |
| Li, C., Ren, Y., Chen, M. Y., Wang, Q., He, Z., Wang, Y. F. (2024). CG9920 is necessary for mitochondrial morphogenesis and individualization during spermatogenesis in Drosophila melanogaster. Dev Biol, 512:13-25 PubMed ID: 38703942
Summary: Drosophila melanogaster is an ideal model organism for investigating spermatogenesis due to its powerful genetics, conserved genes and visible morphology of germ cells during sperm production. Previous work revealed that ocnus (ocn) knockdown resulted in male sterility, and CG9920 was identified as a significantly downregulated protein in fly abdomen after ocn knockdown, suggesting a role of CG9920 in male reproduction. This study found that CG9920 was highly expressed in fly testes. CG9920 knockdown in fly testes caused male infertility with no mature sperms in seminal vesicles. Immunofluorescence staining showed that depletion of CG9920 resulted in scattered spermatid nuclear bundles, fewer elongation cones that did not migrate to the anterior region of the testis, and almost no individualization complexes. Transmission electron microscopy revealed that CG9920 knockdown severely disrupted mitochondrial morphogenesis during spermatogenesis. Notably, CG9920 might not directly interact with Ocn, but rather was inhibited by STAT92E, which itself was indirectly affected by Ocn. A possible novel pathway essential for spermatogenesis in D. melanogaster is proposed whereby Ocn indirectly induces CG9920 expression, potentially counteracting its inhibition by the JAK-STAT signaling pathway. | Bai, Y., Lv, Y. N., Zeng, M., Yan, Z. Y., Huang, D. Y., Wen, J. Z., Lu, H. N., Zhang, P. Y., Wang, Y. F., Ban, N., Yuan, D. W., Li, S., Luan, Y. X. (2024). E93 is indispensable for reproduction in ametabolous and hemimetabolous insects. Development, 151(20) PubMed ID: 38646855
Summary: Ecdysone-induced protein 93 (E93), known as the 'adult-specifier' transcription factor in insects, triggers metamorphosis in both hemimetabolous and holometabolous insects. Although E93 is conserved in ametabolous insects, its spatiotemporal expression and physiological function remain poorly understood. This study first discover that, in the ametabolous firebrat Thermobia domestica, the previtellogenic ovary exhibits cyclically high E93 expression, and E93 mRNA is broadly distributed in previtellogenic ovarioles. E93 homozygous mutant females of T. domestica exhibit severe fecundity deficiency due to impaired previtellogenic development of the ovarian follicles, likely because E93 induces the expression of genes involved in ECM (extracellular matrix)-receptor interactions during previtellogenesis. Moreover, this study reveals that in the hemimetabolous cockroach Blattella germanica, E93 similarly promotes previtellogenic ovarian development. In addition, E93 is also essential for vitellogenesis that is necessary to guarantee ovarian maturation and promotes the vitellogenesis-previtellogenesis switch in the fat body of adult female cockroaches. These findings deepen the understanding of the roles of E93 in controlling reproduction in insects, and of E93 expression and functional evolution, which are proposed to have made crucial contributions to the origin of insect metamorphosis. |
| Samuels, T. J., Gui, J., Gebert, D., Teixeira, K. F. (2024). Two distinct waves of transcriptome and translatome changes drive Drosophila germline stem cell differentiation. The EMBO journal, 43(8):1591-1617 PubMed ID: 38480936
Summary: The tight control of fate transitions during stem cell differentiation is essential for proper tissue development and maintenance. However, the challenges in studying sparsely distributed adult stem cells in a systematic manner have hindered efforts to identify how the multilayered regulation of gene expression programs orchestrates stem cell differentiation in vivo. This study synchronised Drosophila female germline stem cell (GSC) differentiation in vivo to perform in-depth transcriptome and translatome analyses at high temporal resolution. This characterisation revealed widespread and dynamic changes in mRNA level, promoter usage, exon inclusion, and translation efficiency. Transient expression of the master regulator, Bam, drives a first wave of expression changes, primarily modifying the cell cycle program. Surprisingly, as Bam levels recede, differentiating cells return to a remarkably stem cell-like transcription and translation program, with a few crucial changes feeding into a second phase driving terminal differentiation to form the oocyte. Altogether, these findings reveal that rather than a unidirectional accumulation of changes, the in vivo differentiation of stem cells relies on distinctly regulated and developmentally sequential waves. | Ng, A. Y. E., Chan, S. N., Pek, J. W. (2024). Genetic compensation between ribosomal protein paralogs mediated by a cognate circular RNA. Cell Rep, 43(5):114228 PubMed ID: 38735045
Summary: Inter-regulation between related genes, such as ribosomal protein (RP) paralogs, has been observed to be important for genetic compensation and paralog-specific functions. However, how paralogs communicate to modulate their expression levels is unknown. This study reports a circular RNA involved in the inter-regulation between RP paralogs RpL22 and RpL22-like during Drosophila spermatogenesis. Both paralogs are mutually regulated by the circular stable intronic sequence RNA (sisRNA) circRpL22(NE,3S) produced from the RpL22 locus. RpL22 represses itself and RpL22-like. Interestingly, circRpL22 binds to RpL22 to repress RpL22-like, but not RpL22, suggesting that circRpL22 modulates RpL22's function. circRpL22 is in turn controlled by RpL22-like, which regulates RpL22 binding to circRpL22 to indirectly modulate RpL22. This circRpL22-centric inter-regulatory circuit enables the loss of RpL22-like to be genetically compensated by RpL22 upregulation to ensure robust male germline development. Thus, this study identifies sisRNA as a possible mechanism of genetic crosstalk between paralogous genes. |
| Box, A. M., Ramesh, N. A., Nandakumar, S., Church, S. J., Prasad, D., Afrakhteh, A., Taichman, R. S., Buttitta, L. (2024). Cell cycle variants during Drosophila male accessory gland development. G3 (Bethesda), 14(7) PubMed ID: 38683731
Summary: The Drosophila melanogaster male accessory gland (AG) is a functional analog of the mammalian prostate and seminal vesicles containing two secretory epithelial cell types, termed main and secondary cells. This tissue is responsible for making and secreting seminal fluid proteins and other molecules that contribute to successful reproduction. The cells of this tissue are binucleate and polyploid, due to variant cell cycles that include endomitosis and endocycling during metamorphosis. This study provides evidence of additional cell cycle variants in this tissue. Main cells of the gland are connected by ring canals that form after the penultimate mitosis, and an additional post-eclosion endocycle required for gland maturation is described that is dependent on juvenile hormone signaling. Evidence is presented that the main cells of the D. melanogaster AG undergo a unique cell cycle reprogramming throughout organ development that results in step-wise cell cycle truncations culminating in cells containing two octoploid nuclei with under-replicated heterochromatin in the mature gland. It is proposeed this tissue as a model to study developmental and hormonal temporal control of cell cycle variants in terminally differentiating tissues. | Lin, C. T., Ting, R. T., Ou, Y. H., Shao, T. L., Lee, M. C. (2024). Protein degradation of Lsd1 is mediated by Bre1 yet opposed by Lsd1-interacting lncRNAs during fly follicle development. iScience, 27(5):109683 PubMed ID: 38655201
Summary: Tissue development, homeostasis, and repair all require efficient progenitor expansion. Lysine-specific demethylase 1 (Lsd1) maintains plastic epigenetic states to promote progenitor proliferation while overexpressed Lsd1 protein causes oncogenic gene expression in cancer cells. However, the precise regulation of Lsd1 protein expression at the molecular level to drive progenitor differentiation remains unclear. Using Drosophila melanogaster oogenesis as an experimental system, this study discovered molecular machineries that modify Lsd1 protein stability in vivo. Through genetic and biochemical analyses, an E3 ubiquitin ligase, Bre1, was identified as required for follicle progenitor differentiation, likely by mediating Lsd1 protein degradation. Interestingly, specific Lsd1-interacting long non-coding RNAs (LINRs) were found to antagonize Bre1-mediated Lsd1 protein degradation. The intricate interplay discovered among the Lsd1 complex, LINRs and Bre1 provides insight into how Lsd1 protein stability is fine-tuned to underlie progenitor differentiation in vivo. |
January 22nd - Disease Models |
| Matsuoka, T., Yoshida, H., Kasai, T., Tozawa, T., Iehara, T., Chiyonobu, T. (2024). alpha-Synuclein pathology in Drosophila melanogaster is exacerbated by haploinsufficiency of Rop: connecting STXBP1 encephalopathy with α-synucleinopathies. Hum Mol Genet, 33(15):1328-1338 PubMed ID: 38692286
Summary: Syntaxin-binding protein 1 (STXBP1: homolog of Drosophila Rop) is a presynaptic protein that plays important roles in synaptic vesicle docking and fusion. STXBP1 haploinsufficiency causes STXBP1 encephalopathy (STXBP1-E), which encompasses neurological disturbances including epilepsy, neurodevelopmental disorders, and movement disorders. Most patients with STXBP1-E present with regression and movement disorders in adulthood, highlighting the importance of a deeper understanding of the neurodegenerative aspects of STXBP1-E. An in vitro study proposed an interesting new role of STXBP1 as a molecular chaperone for α-Synuclein (αSyn), a key molecule in the pathogenesis of neurodegenerative disorders. However, no studies have shown αSyn pathology in model organisms or patients with STXBP1-E. This study used Drosophila models to examine the effects of STXBP1 haploinsufficiency on α-syn induced neurotoxicity in vivo. Haploinsufficiency of Ras opposite (Rop), the Drosophila ortholog of STXBP1, exacerbates compound eye degeneration, locomotor dysfunction, and dopaminergic neurodegeneration in αSyn-expressing flies. This phenotypic aggravation was associated with a significant increase in detergent-insoluble &lpha;Syn levels in the head. Furthermore, whether trehalose, which has neuroprotective effects in various models of neurodegenerative disorders, mitigates αsyn-induced neurotoxicity exacerbated by Rop haploinsufficiency. In flies expressing αSyn and carrying a heterozygous Rop null variant, trehalose supplementation effectively alleviates neuronal phenotypes, accompanied by a decrease in detergent-insoluble &alphapSyn in the head. In conclusion, this study revealed that Rop haploinsufficiency exacerbates αSyn-induced neurotoxicity by altering the αSyn aggregation propensity. This study not only contributes to understanding the mechanisms of neurodegeneration in STXBP1-E patients, but also provides new insights into the pathogenesis of α-synucleinopathies. | Wangler, M. F., Chao, Y. H., Roth, M., Welti, R., McNew, J. A. (2024). Drosophila Models Uncover Substrate Channeling Effects on Phospholipids and Sphingolipids in Peroxisomal Biogenesis Disorders. bioRxiv, PubMed ID: 38746221
Summary: Peroxisomal Biogenesis Disorders Zellweger Spectrum (PBD-ZSD) disorders are a group of autosomal recessive defects in peroxisome formation that produce a multi-systemic disease presenting at birth or in childhood. Well documented clinical biomarkers such as elevated very long chain fatty acids (VLCFA) are key biochemical diagnostic findings in these conditions. Additional, secondary biochemical alterations such as elevated very long chain lysophosphatidylcholines are allowing newborn screening for peroxisomal disease. In addition, a more widespread impact on metabolism and lipids is increasingly being documented by metabolomic and lipidomic studies. This study utilized Drosophila models of pex2 and pex16 as well as human plasma from individuals with PEX1 mutations. Phospholipid abnormalities were identified in Drosophila larvae and brain characterized by differences in the quantities of phosphatidylcholine (PC) and phosphatidylethanolamines (PE) with long chain lengths and reduced levels of intermediate chain lengths. For diacylglycerol (DAG) the precursor of PE and PC through the Kennedy pathway, the intermediate chain lengths are increased suggesting an imbalance between DAGs and PE and PC that suggests the two acyl chain pools are not in equilibrium. Altered acyl chain lengths are also observed in PE ceramides in the fly models. Interestingly, plasma from human subjects exhibit phospholipid alterations similar to the fly model. Moreover, human plasma shows reduced levels of sphingomyelin with 18 and 22 carbon lengths but normal levels of C24. These results suggest that peroxisomal biogenesis defects alter shuttling of the acyl chains of multiple phospholipid and ceramide lipid classes, whereas DAG species with intermediate fatty acids are more abundant. These data suggest an imbalance between de novo synthesis of PC and PE through the Kennedy pathway and remodeling of existing PC and PE through the Lands cycle. This imbalance is likely due to overabundance of very long and long acyl chains in PBD and a subsequent imbalance due to substrate channeling effects. Given the fundamental role of phospholipid and sphingolipids in nervous system functions, these observations suggest PBD-ZSD are diseases characterized by widespread cell membrane lipid abnormalities. |
| Petitgas, C., Seugnet, L., Dulac, A., Matassi, G., Mteyrek, A., Fima, R., Strehaiano, M., Dagorret, J., Cherif-Zahar, B., Marie, S., Ceballos-Picot, I., Birman, S. (2024). Metabolic and neurobehavioral disturbances induced by purine recycling deficiency in Drosophila. Elife, 12 PubMed ID: 38700995
Summary: Adenine phosphoribosyltransferase (APRT) and hypoxanthine-guanine phosphoribosyltransferase (HGPRT) are two structurally related enzymes involved in purine recycling in humans. Inherited mutations that suppress HGPRT activity are associated with Lesch-Nyhan disease (LND), a rare X-linked metabolic and neurological disorder in children, characterized by hyperuricemia, dystonia, and compulsive self-injury. LND-related mechanisms were studied in the fruit fly. By combining enzymatic assays and phylogenetic analysis, it was confirmed that no HGPRT activity is expressed in Drosophila melanogaster, making the APRT homolog (Aprt) the only purine-recycling enzyme in this organism. Whereas APRT deficiency does not trigger neurological defects in humans, Drosophila Aprt mutants show both metabolic and neurobehavioral disturbances, including increased uric acid levels, locomotor impairments, sleep alterations, seizure-like behavior, reduced lifespan, and reduction of adenosine signaling and content. Locomotor defects could be rescued by Aprt re-expression in neurons and reproduced by knocking down Aprt selectively in the protocerebral anterior medial (PAM) dopaminergic neurons, the mushroom bodies, or glia subsets. Ingestion of allopurinol rescued uric acid levels in Aprt-deficient mutants but not neurological defects, as is the case in LND patients, while feeding adenosine or N(6)-methyladenosine (m(6)A) during development fully rescued the epileptic behavior. Intriguingly, pan-neuronal expression of an LND-associated mutant form of human HGPRT (I42T), but not the wild-type enzyme, resulted in early locomotor defects and seizure in flies, similar to Aprt deficiency. Overall, these results suggest that Drosophila could be used in different ways to better understand LND and seek a cure for this dramatic disease. | Bankapalli, K., Thomas, R. E., Vincow, E. S., Milstein, G., Fisher, L. V., Pallanck, L. J. (2024). A Drosophila model for mechanistic investigation of tau protein spread. bioRxiv, PubMed ID: 38712083
Summary: Brain protein aggregates are a hallmark of neurodegenerative disease. Previous work indicates that specific protein components of these aggregates are toxic, including Tau in Alzheimer's disease and related tauopathies. Increasing evidence also indicates that these toxic proteins traffic between cells in a prion-like fashion, thereby spreading pathology from one brain region to another. However, the mechanisms involved in trafficking are poorly understood. This study therefore developed a transgenic Drosophila model to facilitate rapid evaluation of candidate Tau trafficking modifiers. This model uses the bipartite Q system to drive co-expression of tau and GFP in the fly eye. Age-dependent tau was found to spread into the brain, represented by detection of tau, but not GFP in the brain. Tau trafficking was observed to be attenuated upon inhibition of the endocytic factor dynamin or the kinase glycogen synthase kinase-3β (GSK-3β). Further work revealed that dynamin promotes Tau uptake in recipient tissues, whereas GSK-3β appears to promote Tau spread via direct phosphorylation of Tau. This robust and flexible system will promote the identification of Tau trafficking components involved in the pathogenesis of neurodegenerative diseases. |
| Zhu, J. Y., van de Leemput, J., Han, Z. (2024). Promoting mitochondrial dynamics by inhibiting the PINK1-PRKN pathway to relieve diabetic nephropathy. Disease models & mechanisms, 17(4) PubMed ID: 38602042
Summary: Diabetes is a metabolic disorder characterized by high blood glucose levels and is a leading cause of kidney disease. Diabetic nephropathy has been attributed to dysfunctional mitochondria. However, many questions remain about the exact mechanism. The structure, function and molecular pathways are highly conserved between mammalian podocytes and Drosophila nephrocytes; therefore, flies on a high-sucrose diet were used to model type 2 diabetic nephropathy. The nephrocytes from flies on a high-sucrose diet showed a significant functional decline and decreased cell size, associated with a shortened lifespan. Structurally, the nephrocyte filtration structure, known as the slit diaphragm, was disorganized. At the cellular level, altered mitochondrial dynamics and dysfunctional mitochondria were found. Regulating mitochondrial dynamics by either genetic modification of the Pink1-Park (mammalian PINK1-PRKN) pathway or treatment with BGP-15, mitigated the mitochondrial defects and nephrocyte functional decline. These findings support a role for Pink1-Park-mediated mitophagy and associated control of mitochondrial dynamics in diabetic nephropathy, and demonstrate that targeting this pathway might provide therapeutic benefits for type 2 diabetic nephropathy. | Diaz, J. E. L., Barcessat, V., Bahamon, C., Hecht, C., Das, T. K., Cagan, R. L. (2024). Functional exploration of copy number alterations in a Drosophila model of triple-negative breast cancer. Disease models & mechanisms, 17(7) PubMed ID: 38721669
Summary: Accounting for 10-20% of breast cancer cases, triple-negative breast cancer (TNBC) is associated with a disproportionate number of breast cancer deaths. One challenge in studying TNBC is its genomic profile: with the exception of TP53 loss, most breast cancer tumors are characterized by a high number of copy number alterations (CNAs), making modeling the disease in whole animals challenging. This study computationally analyzed 186 CNA regions previously identified in breast cancer tumors to rank genes within each region by likelihood of acting as a tumor driver. Then a Drosophila p53-Myc TNBC model was used to identify 48 genes as functional drivers. To demonstrate the utility of this functional database, six 3-hit models were established; altering candidate genes led to increased aspects of transformation as well as resistance to the chemotherapeutic drug fluorouracil. This work provides a functional database of CNA-associated TNBC drivers, and a template for an integrated computational/whole-animal approach to identify functional drivers of transformation and drug resistance within CNAs in other tumor types. |
Tuesday, January 21th - Evolutionary homologs |
| Nguyen, T. N. M., Choo, A., Baxter, S. W. (2024). Conservation of shibire and RpII215 temperature-sensitive lethal mutations between Drosophila and Bactrocera tryoni. Frontiers in insect science, 4:1249103 PubMed ID: 38469341
Summary: The sterile insect technique can suppress and eliminate population outbreaks of the Australian horticultural pest, Bactrocera tryoni, the Queensland fruit fly. Sterile males mate with wild females that produce inviable embryos, causing population suppression or elimination. Current sterile insect releases are mixed sex, as the efficient removal of unrequired factory-reared females is not yet possible. This paper assessed the known Drosophila melanogaster temperature-sensitive embryonic lethal alleles shibireG268D, shits1) and RNA polymerase II 215 R977C, RpII215ts)) for potential use in developing B. tryoni genetic sexing strains (GSS) for the conditional removal of females. Complementation tests in D. melanogaster wild-type or temperature-sensitive genetic backgrounds were performed using the GAL4-UAS transgene expression system. A B. tryoni wild-type shibire isoform partially rescued Drosophila temperature lethality at 29°C by improving survivorship to pupation, while expressing B. tryoni shits1 failed to rescue the lethality, supporting a temperature-sensitive phenotype. Expression of the B. tryoni RpII215 wild-type protein rescued the lethality of D. melanogaster RpII215(ts) flies at 29°C. Overexpressing the B. tryoni RpII215(ts) allele in the D. melanogaster wild-type background unexpectedly produced a dominant lethal phenotype at 29°C. The B. tryoni shibire and RpII215 wild-type alleles were able to compensate, to varying degrees, for the function of the D. melanogaster temperature-sensitive proteins, supporting functional conservation across species. Shibire and RpII215 hold potential for developing insect strains that can selectively kill using elevated temperatures; however, alleles with milder effects than shits1 will need to be considered. | Rredhi, A., Petersen, J., Wagner, V., Vuong, T., Li, W., Li, W., Schrader, L., Mittag, M. (2024). The UV-A Receptor CRY-DASH1 Up- and Downregulates Proteins Involved in Different Plastidial Pathways. J Mol Biol, 436(5):168271 PubMed ID: 37699454
Summary: Algae encode up to five different types of cryptochrome photoreceptors. So far, relatively little is known about the biological functions of the DASH (Drosophila, Arabidopsis, Synechocystis and Homo)-type cryptochromes. The green alga Chlamydomonas reinhardtii encodes two of them. CRY-DASH1 also called DCRY1 has its maximal absorption peak in the UV-A range. It is localized in the chloroplast and plays an important role in balancing the photosynthetic machinery. A comparative analysis of chloroplast proteins from wild type and a knockout mutant of CRY-DASH1 named cry-dash1(mut) was performed, using label-free quantitative proteomics as well as immunoblotting. The results show upregulation of enzymes involved in specific pathways in the mutant including key enzymes of chlorophyll and carotenoid biosynthesis consistent with increased levels of photosynthetic pigments in cry-dash1(mut). There is also an increase in certain redox as well as photosystem I and II proteins, including D1. Strikingly, CRY-DASH1 is coregulated in a D1 deletion mutant, where its amount is increased. In contrast, key proteins of the central carbon metabolism, including glycolysis/gluconeogenesis, dark fermentation and the oxidative pentose phosphate pathway are downregulated in cry-dash1(mut). Similarly, enzymes of histidine biosynthesis are downregulated in cry-dash1(mut) leading to a reduction in the amount of free histidine. Yet, transcripts encoding for several of these proteins are at a similar level in the wild type and cry-dash1(mut) or even opposite. CRY-DASH1 can bind to RNA, taking the psbA RNA encoding D1 as target. These data suggest that CRY-DASH1 regulates plastidial metabolic pathways at the posttranscriptional level. |
| Zhang, G., Zheng, C., Ding, Y. H., Mello, C. (2024). Casein kinase II promotes piRNA production through direct phosphorylation of USTC component TOFU-4. Nat Commun, 15(1):2727 PubMed ID: 38548791
Summary: Piwi-interacting RNAs (piRNAs) are genomically encoded small RNAs that engage Piwi Argonaute proteins to direct mRNA surveillance and transposon silencing. Despite advances in understanding piRNA pathways and functions, how the production of piRNA is regulated remains elusive. Using a genetic screen this studyidentified identify Casein kinase II (CK2) as a factor required for piRNA pathway function. CK2 is shown to be required for the localization of PRG-1 and for the proper localization of several factors that comprise the 'upstream sequence transcription complex' (USTC), which is required for piRNA transcription. Loss of CK2 impairs piRNA levels suggesting that CK2 promotes USTC function. The USTC component twenty-one-U was found to foul-up 4 (TOFU-4) as a direct substrate for CK2. Our findings suggest that phosphorylation of TOFU-4 by CK2 promotes the assembly of USTC and piRNA transcription. Notably, during the aging process, CK2 activity declines, resulting in the disassembly of USTC, decreased piRNA production, and defects in piRNA-mediated gene silencing, including transposons silencing. These findings highlight the significance of posttranslational modification in regulating piRNA biogenesis and its implications for the aging process. Overall, our study provides compelling evidence for the involvement of a posttranslational modification mechanism in the regulation of piRNA biogenesis. | Hou, C., Zhang, A., Jin, Y., Ye, C., Li, R., Liu, Z., Gao, J. (2024). Role of LGL1 in cerebellar primordium of embryonic mice. Neuroreport, 35(6):374-379 PubMed ID: 38526932
Summary: Lethal giant larvae 1 (LGL1) is originally recognized as a tumor suppressor, implicated in maintaining cell polarity in Drosophila and mammalian cells. Cell polarity plays a crucial role in tumorigenesis. Pax2-LGL1 >-/- conditional knockout mice were previously established, but focus was not placed on the tumorigenesis in cerebellar primordium. HE staining was used to detect the morphological structure of the cerebellar primordium during early embryonic development in Pax2-LGL1 -/- mice. Immunofluorescence assays were used to detect the expression of polar molecules. TUNEL staining assessed tissue apoptosis. Our findings reveal that deletion of LGL1 leads to the emergence of neuroblastoma-like tissues within the cerebellum primordium during early embryogenesis. This outcome can be attributed to alterations in expression patterns of polar molecules Cdc42 and β-catenin following early deletion of LGL1, resulting in loss of cell polarity among neuroepithelial cells and subsequent formation of tumor-like tissues. However, further histological examination demonstrated that these tumor-like tissues disappear from embryonic day 15.5 onwards within the cerebellar primordium of Pax2-LGL1 -/- mice due to apoptosis-mediated cellular compensation. Our data emphasize the importance of LGL1 in maintaining neuroepithelial cell polarity and reveal a novel role for LGL1 in regulating tumorigenesis and ablation in the cerebellar primordium. |
| Montalvo-Mendez, R. J., Cardenas-Tueme, M., Resendez-Perez, D. (2024). Drosophila in the study of hTBP protein interactions in the development and modeling of SCA17. Gaceta medica de Mexico, 160(1):1-8 PubMed ID: 38753562
Summary: Protein interactions participate in many molecular mechanisms involved in cellular processes. The human TATA box binding protein (hTBP: see drosophila TBA) interacts with Antennapedia (Antp) through its N-terminal region, specifically via its glutamine homopeptides. This PolyQ region acts as a binding site for other transcription factors under normal conditions, but when it expands, it generates spinocerebellar ataxia 17 (SCA17), whose protein aggregates in the brain prevent its correct functioning. To determine whether the hTBP glutamine-rich region is involved in its interaction with homeoproteins and the role it plays in the formation of protein aggregates in SCA17. This study characterized hTBP interaction with other homeoproteins. hTBP interacted with homeoproteins through its glutamine-rich region, and hTBP protein aggregates with expanded glutamines were found to affect the locomotor capacity of flies. The study of hTBP interactions opens the possibility for the search for new therapeutic strategies in neurodegenerative pathologies such as SCA17. | Toraason, K., Johnson, N., Guernsey, J., Laughon, A. (2024). Vertebrate-conserved Schnurri zinc fingers restrain Drosophila vein patterning. microPublication biology, 2024 PubMed ID: 38344065
Summary: The Drosophila Smad-interacting co-factor, Schnurri (Shn) confers transcriptional repression in response to Decapentaplegic (Dpp) signaling. Shn zinc fingers 6-8 mediate this Smad interaction but are lacking in vertebrate Shn homologs. In contrast, the vertebrate-conserved zinc finger 1,2 and 4,5 pairs have been reported to engage in Smad-mediated transcriptional activation in fly and vertebrate systems, and to contribute to Dpp-dependent tissue repair in the fly retina. This study reports that mutation of zinc coordination residues within vertebrate-conserved Shn zinc finger pairs 1,2 and 4,5 results in ectopic venation that is sensitive to Dpp signaling. |
Friday, January 17th - Autophagy and Apoptosis |
| Peralta, J., DuPriest, B., Orozco, D., Pacheco, J. R., Martins, L., Soriano, R. A., Wong, A., Wong, R., Grillo-Hill, B. (2024). Drosophila Nhe2 overexpression induces autophagic cell death. Mol Biol Cell, 35(7):br13 PubMed ID: 38696256
Summary: Autophagy is a conserved catabolic process where double membrane-bound structures form around macromolecules or organelles targeted for degradation. Autophagosomes fuse with lysosomes to facilitate degradation and macromolecule recycling for homeostasis or growth in a cell autonomous manner. In cancer cells, autophagy is often up-regulated and helps cancer cells survive nutrient deprivation and stressful growth conditions. This study proposes that the increased intracellular pH (pHi) common to cancer cells is sufficient to induce autophagic cell death. Tools were developed in previous work to increase pHi in the Drosophila eye via overexpression of DNhe2, resulting in aberrant patterning and reduced tissue size. Fly eyes were examined at earlier stages of development, and fewer interommatidial cells were found. Whether this decrease in cell number was due to increased cell death was examined. The DNhe2-induced cell death was caspase independent, which is inconsistent with apoptosis. However, this cell death required autophagy genes, which supports autophagy as the mode of cell death. Expression of molecular markers supports increased autophagy. Together, these findings suggest new roles for ion transport proteins in regulating conserved, critical developmental processes and provide evidence for new paradigms in growth control. | Ahmed-de-Prado, S., Estella, C., Baonza, A. (2024). Temporal dynamics of apoptosis-induced proliferation in pupal wing development: implications for regenerative ability. BMC Biol, 22(1):98 PubMed ID: 38679694
Summary: wing imaginal discs are epithelial structures that can regenerate after tissue injury. While significant research has focused on investigating regenerative responses during larval stages, comprehension of the regenerative potential of pupal wings and the underlying mechanisms contributing to the decline of regenerative responses remains limited. This study explored the temporal dynamics during pupal development of the proliferative response triggered by the induction of cell death, a typical regenerative response. The results indicate that the apoptosis-induced proliferative response can continue until 34 h after puparium formation (APF), beyond this point cell death alone is not sufficient to induce a regenerative response. Under normal circumstances, cell proliferation ceases around 24 h APF. Interestingly, the failure of reinitiating the cell cycle beyond this time point is not attributed to an incapacity to activate the JNK pathway. Instead, the results suggest that the function of the ecdysone-responsive transcription factor E93 is involved in limiting the apoptosis-induced proliferative response during pupal development. This study shows that apoptosis can prolong the proliferative period of cells in the wing during pupal development as late as 34 h APF, at least 10 h longer than during normal development. After this time point, the regenerative response is diminished, a process mediated in part by the ecdysone-responsive transcription factor E93. |
| Szypulski, K., Tyszka, A., Pyza, E., Damulewicz, M. (2024). Autophagy as a new player in the regulation of clock neurons physiology of Drosophila melanogaster. Sci Rep, 14(1):6085 PubMed ID: 38480808
Summary: Axonal terminals of the small ventral lateral neurons (sLNvs), the circadian clock neurons of Drosophila, show daily changes in their arborization complexity, with many branches in the morning and their shrinkage during the night. This complex phenomenon is precisely regulated by several mechanisms. This study describes that one of them is autophagy, a self-degradative process, also involved in changes of cell membrane size and shape. The results showed that autophagosome formation and processing in PDF-expressing neurons (both sLNv and lLNv) are rhythmic and they have different patterns in the cell bodies and terminals. These rhythmic changes in the autophagy activity seem to be important for neuronal plasticity. Autophagosome cargos are different during the day and night, and more proteins involved in membrane remodeling are present in autophagosomes in the morning. In addition, Atg8-positive vesicles are also present outside the sLNv terminals, which suggests that secretory autophagy might be involved in regulating the clock signaling network. These data indicate that rhythmic autophagy in clock neurons affect the pacemaker function, through remodeling of terminal membrane and secretion of specific proteins from sLNvs. | Dresselhaus, E. C., Harris, K. P., Blanchette, C. R., Koles, K., Del Signore, S. J., Pescosolido, M. F., Ermanoska, B., Rozencwaig, M., Soslowsky, R. C., Parisi, M. J., Stewart, B. A., Mosca, T. J., Rodal, A. A. (2024). ESCRT disruption provides evidence against trans-synaptic signaling via extracellular vesicles. J Cell Biol, 223(9) PubMed ID: 38842573
Summary: Extracellular vesicles (EVs) are released by many cell types, including neurons, carrying cargoes involved in signaling and disease. It is unclear whether EVs promote intercellular signaling or serve primarily to dispose of unwanted materials. This study shows that loss of multivesicular endosome-generating endosomal sorting complex required for transport (ESCRT) machinery disrupts release of EV cargoes from Drosophila motor neurons. Surprisingly, ESCRT depletion does not affect the signaling activities of the EV cargo Synaptotagmin-4 (Syt4) and disrupts only some signaling activities of the EV cargo Evenness interrupted (Evi). Thus, these cargoes may not require intercellular transfer via EVs, and instead may be conventionally secreted or function cell-autonomously in the neuron. EVs are phagocytosed by glia and muscles, and ESCRT disruption causes compensatory autophagy in presynaptic neurons, suggesting that EVs are one of several redundant mechanisms to remove cargoes from synapses. These results suggest that synaptic EV release serves primarily as a proteostatic mechanism for certain cargoes. |
| Xu, Y., Liu, W., Sun, Z., Yu, Y., Yang, T., Lu, X., Zhang, G., Jiao, J., Duan, X. (2024). The two autophagy-related proteins 8a and 8b play distinct physiological roles in Drosophila. Genomics, 116(3):110853 PubMed ID: 38701988
Summary: Atg8 family proteins play crucial roles in autophagy to maintain cellular homeostasis. However, the physiological roles of Atg8 family proteins have not been systematically determined. This study generated Atg8a and Atg8b (homologs of Atg8 in Drosophila melanogaster) knockout flies. The loss of Atg8a affected autophagy and resulted in partial lethality, abnormal wings, decreased lifespan, and decreased climbing ability in flies. Furthermore, the loss of Atg8a resulted in reduced muscle integrity and the progressive degeneration of the neuron system. The phosphorylation at Ser88 of Atg8a is important for autophagy and neuronal integrity. The loss of Atg8b did not affect autophagy but induced male sterility in flies. This study took full advantage of the fly system to elucidate the physiological function of Atg8a and Atg8b in Drosophila. | Zhang, J., Tang, T., Zhang, R., Wen, L., Deng, X., Xu, X., Yang, W., Jin, F., Cao, Y., Lu, Y., Yu, X. Q. (2024). Maintaining Toll signaling in Drosophila brain is required to sustain autophagy for dopamine neuron survival. iScience, 27(2):108795 PubMed ID: 38292423
Summary: Macroautophagy/autophagy is a conserved process in eukaryotic cells to degrade and recycle damaged intracellular components. Higher level of autophagy in the brain has been observed, and autophagy dysfunction has an impact on neuronal health, but the molecular mechanism is unclear. This study showed that overexpression of Toll-1 and Toll-7 receptors, as well as active Spatzle proteins in Drosophila S2 cells enhanced autophagy, and Toll-1/Toll-7 activated autophagy was dependent on Tube-Pelle-PP2A. Interestingly, Toll-1 but not Toll-7 mediated autophagy was dMyd88 dependent. Importantly, loss of functions in Toll-1 and Toll-7 receptors and PP2A activity in flies decreased autophagy level, resulting in the loss of dopamine (DA) neurons and reduced fly motion. These results indicated that proper activation of Toll-1 and Toll-7 pathways and PP2A activity in the brain are necessary to sustain autophagy level for DA neuron survival. |
Thursday, January 16th - Enhancers and Transcriptional regulation |
| Schwartz, M. B., Prudnikova, M. M., Andreenkov, O. V., Volkova, E. I., Zhimulev, I. F., Antonenko, O. V., Demakov, S. A. (2024). Transcription factor DREF regulates expression of the microRNA gene bantam in Drosophila melanogaster. Vavilovskii zhurnal genetiki i selektsii, 28(2):131-137 PubMed ID: 38680180
Summary: The bantam gene encodes a vital microRNA and has a complex expression pattern in various tissues at different stages of Drosophila development. This microRNA is involved in the control of normal development of the ocular and wing imaginal discs, the central nervous system, and also in maintaining the undifferentiated state of stem cells in the ovaries of adult females. At the cellular level, bantam stimulates cell proliferation and prevents apoptosis. The bantam gene is a target of several conserved signaling cascades, in particular, Hippo. At the moment, at least ten proteins are known to directly regulate the expression of this gene in different tissues of Drosophila. This study found that the bantam regulatory region contains motifs characteristic of binding sites for DREF, a transcription factor that regulates the expression of Hippo cascade genes. Using transgenic lines containing a full-length bantam lethality-rescuing deletion fragment and a fragment with a disrupted DREF binding site, this study showed that these motifs are functionally significant because their disruption at the bantam locus reduces expression levels in the larvae and ovaries of homozygous flies, which correlates with reduced vitality and fertility. The effect of DREF binding to the promoter region of the bantam gene on its expression level suggests an additional level of complexity in the regulation of expression of this microRNA. A decrease in the number of eggs laid and a shortening of the reproductive period in females when the DREF binding site in the regulatory region of the bantam gene is disrupted suggests that, through bantam, DREF is also involved in the regulation of Drosophila oogenesis. | Rice, G., Gaitan-Escudero, T., Charles-Obi, K., Zeitlinger, J., Rebeiz, M. (2024). Gene regulatory network co-option is sufficient to induce a morphological novelty in Drosophila. bioRxiv, PubMed ID: 38585823
Summary: Identifying the molecular origins by which new morphological structures evolve is one of the long standing problems in evolutionary biology. To date, vanishingly few examples provide a compelling account of how new morphologies were initially formed, thereby limiting understanding of how diverse forms of life derived their complex features. This study provides evidence that the large projections on the Drosophila eugracilis phallus that are implicated in sexual conflict have evolved through co-option of the trichome genetic network. These unicellular apical projections on the phallus postgonal sheath are reminiscent of trichomes that cover the Drosophila body but are up to 20-fold larger in size. During their development, they express the transcription factor Shavenbaby, the master regulator of the trichome network. Consistent with the co-option of the Shavenbaby network during the evolution of the D. eugracilis projections, somatic mosaic CRISPR/Cas9 mutagenesis shows that shavenbaby is necessary for their proper length. Moreover, mis-expression of Shavenbaby in the sheath of D. melanogaster, a naive species that lacks these extensions, is sufficient to induce small trichomes. These induced extensions rely on a genetic network that is shared to a large extent with the D. eugracilis projections, indicating its co-option but also some genetic rewiring. Thus, by leveraging a genetically tractable evolutionarily novelty, this work shows that the trichome-forming network is flexible enough that it can be co-opted in a new context, and subsequently refined to produce unique apical projections that are barely recognizable compared to their simpler ancestral beginnings. |
| Ma, D., Ojha, P., Yu, A. D., Araujo, M. S., Luo, W., Keefer, E., Díaz, M. M., Wu, M., Joiner, W. J., Abruzzi, K. C., Rosbash, M. (2024). Timeless noncoding DNA contains cell-type preferential enhancers important for proper Drosophila circadian regulation. Proc Natl Acad Sci U S A, 121(15):e2321338121 PubMed ID: 38568969
Summary: To address the contribution of transcriptional regulation to Drosophila clock gene expression and to behavior, a series of CRISPR-mediated deletions were generated within two regions of the circadian gene timeless (tim), an intronic E-box region and an upstream E-box region that are both recognized by the key transcription factor Clock (Clk) and its heterodimeric partner Cycle. The upstream deletions but not an intronic deletion dramatically impact tim expression in fly heads; the biggest upstream deletion reduces peak RNA levels and tim RNA cycling amplitude to about 15% of normal, and there are similar effects on Tim protein. The cycling amplitude of other clock genes is also strongly reduced, in these cases due to increases in trough levels. These data underscore the important contribution of the upstream E-box enhancer region to tim expression and of Tim to clock gene transcriptional repression in fly heads. Surprisingly, tim expression in clock neurons is only modestly affected by the biggest upstream deletion and is similarly affected by a deletion of the intronic E-box region. This distinction between clock neurons and glia is paralleled by a dramatically enhanced accessibility of the intronic enhancer region within clock neurons. This distinctive feature of tim chromatin was revealed by ATAC-seq (assay for transposase-accessible chromatin with sequencing) assays of purified neurons and glia as well as of fly heads. The enhanced cell type-specific accessibility of the intronic enhancer region explains the resilience of clock neuron tim expression and circadian behavior to deletion of the otherwise more prominent upstream tim E-box region. | Vanderperre, S., Merabet, S. (2024). Visualization of the Association of Dimeric Protein Complexes on Specific Enhancers in the Salivary Gland Nuclei of Drosophila Larva. Cells, 13(7) PubMed ID: 38607052
Summary: Transcription factors (TFs) regulate gene expression by recognizing specific target enhancers in the genome. The DNA-binding and regulatory activity of TFs depend on the presence of additional protein partners, leading to the formation of versatile and dynamic multimeric protein complexes. Visualizing these protein-protein interactions (PPIs) in the nucleus is key for decrypting the molecular cues underlying TF specificity in vivo. Over the last few years, Bimolecular Fluorescence Complementation (BiFC) has been developed in several model systems and applied in the analysis of different types of PPIs. In particular, BiFC has been applied when analyzing PPIs with hundreds of TFs in the nucleus of live Drosophila embryos. However, the visualization of PPIs at the level of specific target enhancers or genomic regions of interest awaits the advent of DNA-labelling methods that can be coupled with BiFC. This study present a novel experimental strategy, called BiFOR, based on the coupling of BiFC with the bacterial ANCHOR DNA-labelling system. BiFOR was demonstrated to enable the precise quantification of the enrichment of specific dimeric protein complexes on target enhancers in Drosophila salivary gland nuclei. Given its versatility and sensitivity, BiFOR could be applied more widely to other tissues during Drosophila development. This work sets up the experimental basis for future applications of this strategy. |
| He, Q., Wang, S., Chen, S., Chen, J. (2024). Juvenile hormone signal transducer hairy inhibits Kruppel homolog1 expression. Biochem Biophys Res Commun, 726:150276 PubMed ID: 38908347
Summary: >Hairy and Kruppel homolog 1 (Kr-h1) are transcriptional repressors that act synergistically to mediate the gene-repressive action of juvenile hormone (JH). However, whether a regulatory relationship exists between Hairy and Kr-h1 remains unclear. In this study, an inhibitory effect of Hairy on Kr-h1 expression was found. Genetic studies in Drosophila have shown that the simultaneous overexpression of Hairy and Kr-h1 can rescue the defective phenotypes caused by the overexpression of a single factor. Reduced expression of Kr-h1 was observed in Hairy-overexpressing flies and cells, whereas the expression levels of Hairy were unaffected in cells with ectopic expression of Kr-h1. The inhibitory effect of Hairy on Kr-h1 expression was found to occur at the transcriptional level, as Hairy bound directly to the B-box within the Kr-h1 promoter via the bHLH motif and recruited the corepressors C-terminal binding protein (CtBP) and Groucho (Gro) through the PLSLV and WRPW motifs, respectively. These findings revealed a regulatory relationship between two JH response factors, which advances our understanding of the molecular mechanism of JH signaling. | Connell, M., Xie, Y., Deng, X., Chen, R., Zhu, S. (2024). Kin17 regulates proper cortical localization of Miranda in Drosophila neuroblasts by regulating Flfl expression. Cell Rep, 43(3):113823 PubMed ID: 38386552
Summary: During asymmetric division of Drosophila larval neuroblasts, the fate determinant Prospero (Pros) and its adaptor Miranda (Mira) are segregated to the basal cortex through atypical protein kinase C (aPKC) phosphorylation of Mira and displacement from the apical cortex, but Mira localization after aPKC phosphorylation is not well understood. This study identified Kin17, a DNA replication and repair protein, as a regulator of Mira localization during asymmetric cell division. Loss of Kin17 leads to aberrant localization of Mira and Pros to the centrosome, cytoplasm, and nucleus. Evidence is provided to show that the mislocalization of Mira and Pros is likely due to reduced expression of Falafel (Flfl), a component of protein phosphatase 4 (PP4), and defects in dephosphorylation of serine-96 of Mira. This work reveals that Mira is likely dephosphorylated by PP4 at the centrosome to ensure proper basal localization of Mira after aPKC phosphorylation and that Kin17 regulates PP4 activity by regulating Flfl expression. |
Wednesday, January 15th - Adult Neural Structure, Development, and Function |
| Babski, H., Codianni, M., Bhandawat, V. (2024). Octopaminergic descending neurons in Drosophila: Connectivity, tonic activity and relation to locomotion.. Heliyon, 10(9):e29952 PubMed ID: 38698992
Summary: Projection neurons that communicate between different brain regions and local neurons that shape computation within a brain region form the majority of all neurons in the brain. Another important class of neurons is neuromodulatory neurons; these neurons are in much smaller numbers than projection/local neurons but have a large influence on computations in the brain. Neuromodulatory neurons are classified by the neurotransmitters they carry, such as dopamine and serotonin. Much of our knowledge of the effect of neuromodulators comes from experiments in which either a large population of neuromodulatory neurons or the entire population is perturbed. Alternatively, a given neuromodulator is exogenously applied. While these experiments are informative of the general role of the neurotransmitter, one limitation of these experiments is that the role of individual neuromodulatory neurons remains unknown. This study investigate the role of a class of octopaminergic (octopamine is the invertebrate equivalent of norepinephrine) neurons in Drosophila or fruit fly. Neuromodulation in Drosophila work along similar principles as humans; and the smaller number of neuromodulatory neurons allowed assessing of the role of individual neurons. This study focuses on a subpopulation of octopaminergic descending neurons (OA-DNs) whose cell bodies are in the brain and project to the thoracic ganglia. Using in-vivo whole-cell patch-clamp recordings and anatomical analyses that allow comparison of light microscopy data to the electron microscopic volumes available in the fly, neurons within each cluster were found to have similar physiological properties, including their relation to locomotion. However, neurons in the same cluster with similar anatomy have very different connectivity. These data are consistent with the hypothesis that each OA-DN is recruited individually and has a unique function within the fly's brain. | Pang, M. M., Chen, F., Xie, M., Druckmann, S., Clandinin, T. R., Yang, H. H. (2024). A recurrent neural circuit in Drosophila deblurs visual inputs. bioRxiv, PubMed ID: 38712245
Summary: A critical goal of vision is to detect changes in light intensity, even when these changes are blurred by the spatial resolution of the eye and the motion of the animal. This study describes a recurrent neural circuit in Drosophila that compensates for blur and thereby selectively enhances the perceived contrast of moving edges. Using in vivo, two-photon voltage imaging, this study measured the temporal response properties of L1 and L2, two cell types that receive direct synaptic input from photoreceptors. These neurons have biphasic responses to brief flashes of light, a hallmark of cells that encode changes in stimulus intensity. However, the second phase was often much larger than the first, creating an unusual temporal filter. Genetic dissection revealed that recurrent neural circuitry strongly shapes the second phase of the response, informing the structure of a dynamical model. By applying this model to moving natural images, it was demonstrated that rather than veridically representing stimulus changes, this temporal processing strategy systematically enhances them, amplifying and sharpening responses. Comparing the measured responses of L2 to model predictions across both artificial and natural stimuli revealed that L2 tunes its properties as the model predicts in order to deblur images. Since this strategy is tunable to behavioral context, generalizable to any time-varying sensory input, and implementable with a common circuit motif, it could be broadly used to selectively enhance sharp and salient changes. |
| Moreno-Sanchez, A., Vasserman, A. N., Jang, H., Hina, B. W., von Reyn, C. R., Ausborn, J. (2024). Morphology and synapse topography optimize linear encoding of synapse numbers in Drosophila looming responsive descending neurons. PubMed ID: 38712267
Summary: Synapses are often precisely organized on dendritic arbors, yet the role of synaptic topography in dendritic integration remains poorly understood. Utilizing electron microscopy (EM) connectomics this study investigated synaptic topography in Drosophila melanogaster looming circuits, focusing on retinotopically tuned visual projection neurons (VPNs) that synapse onto descending neurons (DNs). Synapses of a given VPN type project to non-overlapping regions on DN dendrites. Within these spatially constrained clusters, synapses are not retinotopically organized, but instead adopt near random distributions. To investigate how this organization strategy impacts DN integration, multicompartment models of DNs were developed fitted to experimental data and using precise EM morphologies and synapse locations. DN dendrite morphologies were found to ormalize EPSP amplitudes of individual synaptic inputs and that near random distributions of synapses ensure linear encoding of synapse numbers from individual VPNs. These findings illuminate how synaptic topography influences dendritic integration and suggest that linear encoding of synapse numbers may be a default strategy established through connectivity and passive neuron properties, upon which active properties and plasticity can then tune as needed. | Wang, Y., Salazar, R. J., Simonetta, L. T., Sorrentino, V., Gatton, T. J., Wu, B., Vecsey, C. G., Carrillo, R. A. (2024). hkb is required for DIP-α expression and target recognition in the Drosophila neuromuscular circuit. Communications biology, 7(1):507 PubMed ID: 38678127
Summary: Nervous systems contains billions of neurons that form precise connections with each other through interactions between cell surface proteins. In Drosophila, the Dpr and DIP immunoglobulin protein subfamilies form homophilic or heterophilic interactions to instruct synaptic connectivity, synaptic growth, and cell survival. However, the upstream regulatory mechanisms of Dprs and DIPs are not clear. On the other hand, while transcription factors have been implicated in target recognition, their downstream cell surface proteins remain mostly unknown. An F1 dominant modifier genetic screen was constructed to identify regulators of Dprs and DIPs. huckebein (hkb), a transcription factor previously implicated in target recognition of the dorsal Is motor neuron was identified. hkb is know to genetically interact with DIP-α and loss of hkb leads to complete removal of DIP-α expression specifically in dorsal Is motor neurons. This specificity was confirmed to be through the dorsal Is motor neuron specific transcription factor, even-skipped (eve), which acts downstream of hkb. Analysis of the genetic interaction between hkb and eve reveals that they act in the same pathway to regulate dorsal Is motor neuron connectivity. This study provides insight into the transcriptional regulation of DIP-&alphha; and suggests that distinct regulatory mechanisms exist for the same CSP in different neurons. |
| Lee, S. J., Dallmann, C. J., Cook, A. P., Tuthill, J. C., Agrawal, S. (2024). Divergent neural circuits for proprioceptive and exteroceptive sensing of the Drosophila leg. bioRxiv, PubMed ID: 38712128
Summary: Somatosensory neurons provide the nervous system with information about mechanical forces originating inside and outside the body. This study used connectomics to reconstruct and analyze neural circuits downstream of the largest somatosensory organ in the Drosophila leg, the femoral chordotonal organ (FeCO). The FeCO has been proposed to support both proprioceptive sensing of the fly's femur-tibia joint and exteroceptive sensing of substrate vibrations, but it remains unknown which sensory neurons and central circuits contribute to each of these functions. Different subtypes of FeCO sensory neurons were found to feed into distinct proprioceptive and exteroceptive pathways. Position- and movement-encoding FeCO neurons connect to local leg motor control circuits in the ventral nerve cord (VNC), indicating a proprioceptive function. In contrast, signals from the vibration-encoding FeCO neurons are integrated across legs and transmitted to auditory regions in the brain, indicating an exteroceptive function. Overall, this analyses reveal the structure of specialized circuits for processing proprioceptive and exteroceptive signals from the fly leg. They also demonstrate how analyzing patterns of synaptic connectivity can distill organizing principles from complex sensorimotor circuits. | Karashchuk, L., Li, J. S. L., Chou, G. M., Walling-Bell, S., Brunton, S. L., Tuthill, J. C., Brunton, B. W. (2024). Sensorimotor delays constrain robust locomotion in a 3D kinematic model of fly walking. bioRxiv. PubMed ID: 38712226
Summary: Walking animals must maintain stability in the presence of external perturbations, despite significant temporal delays in neural signaling and muscle actuation. This study develop a 3D kinematic model with a layered control architecture to investigate how sensorimotor delays constrain robustness of walking behavior in the fruit fly, Drosophila. Motivated by the anatomical architecture of insect locomotor control circuits, this model consists of three component layers: a neural network that generates realistic 3D joint kinematics for each leg, an optimal controller that executes the joint kinematics while accounting for delays, and an inter-leg coordinator. The model generates realistic simulated walking that matches real fly walking kinematics and sustains walking even when subjected to unexpected perturbations, generalizing beyond its training data. However, it was found that the model's robustness to perturbations deteriorates when sensorimotor delay parameters exceed the physiological range. These results suggest that fly sensorimotor control circuits operate close to the temporal limit at which they can detect and respond to external perturbations. More broadly, this study showed how a modular, layered model architecture can be used to investigate physiological constraints on animal behavior. |
Tuesday - January 14th - Behavior |
| Prunier, A., Trannoy, S. (2024). Learning from fights: Males' social dominance status impact reproductive success in Drosophila melanogaster. PLoS One, 19(3):e0299839 PubMed ID: 38452142
Summary: In animals, the access to vital resources often relies on individuals' behavioural personality, strength, motivation, past experiences and dominance status. Dominant individuals would be more territorial, providing them with a better access to food resources and mate. The so-called winner and loser effects induce individuals' behavioural changes after experiencing a victory or a defeat, and lead to an individual persistent state influencing the outcome of subsequent fights. However, whether and how development of winner and loser effects affect individuals' fitness is controversial. The aim of this study is to evaluate how individuals' fitness can be influenced by previous fighting experience in Drosophila melanogaster. This study assessed various behavioural performances as indicators for dominant and subordinate fitness. These results show that subordinates are less territorial than dominants although their locomotor abilities are not affected. It was also demonstrated that in a non-competitive context, experiencing a defeat reduces males' motivation to court females but not the reproductive success while in a competitive context, it negatively affects males' reproductive success. However, no impact was found upon either males' ability to distinguish potential mates nor on females' choice of a specific mating partner. Overall, these results indicate that previous defeats reduce reproductive success, a commonly used estimate of individual fitness. | Gattuso, H., Nuanz, K., de la Rea, B., Ermentrout, B., Victor, J., Nagel, K. (2024). Inhibitory control of locomotor statistics in walking Drosophila. bioRxiv, PubMed ID: 38659800
Summary: In order to forage for food, many animals regulate not only specific limb movements but the statistics of locomotor behavior over time, for example switching between long-range dispersal behaviors and more localized search depending on the availability of resources. How pre-motor circuits regulate such locomotor statistics is not clear. This study took advantage of the robust changes in locomotor statistics evoked by attractive odors in walking Drosophila to investigate their neural control. This study began by analyzing the statistics of ground speed and angular velocity. During search behavior, flies adopt higher angular velocities and slower ground speeds, and tend to turn for longer periods of time in one direction. It was further found that flies spontaneously adopt periods of different mean ground speed, and that these changes in state influence the length of odor-evoked runs. Next a simple physiologically-inspired computational model of locomotor control was developed that can recapitulate these statistical features of fly locomotion. This model suggests that contralateral inhibition plays a key role both in regulating the difference between baseline and search behavior, and in modulating the response to odor with ground speed. As the fly connectome predicts decussating inhibitory neurons in the lateral accessory lobe (LAL), a pre-motor structure, genetic tools were generated to target these neurons and test their role in behavior. Consistent with this model, activation of neurons labeled in one line was found to increased curvature. In a second line labeling distinct neurons, activation and inactivation strongly and reciprocally regulated ground speed and altered the length of the odor-evoked run. Together, this work develops a biologically plausible computational architecture that captures the statistical features of fly locomotion across behavioral states and identifies potential neural substrates of these computations. |
| Peckenpaugh, B., Yew, J. Y., Moyle, L. C. (2024). Long-sperm precedence and other cryptic female choices in Drosophila melanogaster. bioRxiv, PubMed ID: 38712086
Summary: Females that mate multiply make postmating choices about which sperm fertilize their eggs (cryptic female choice); however, the male characteristics they use to make such choices remain unclear. This study sought to understand female sperm use patterns by evaluating whether Drosophila melanogaster females adjust sperm use (second male paternity) in response to four main factors: male genotype, male courtship effort, male pheromone alteration, and male postmating reproductive morphology. The experiment was replicated across four different D. melanogaster lines, in a full factorial design, including a pheromone manipulation in which second males were perfumed to resemble heterospecific (D. yakuba) males. Females prefer longer sperm-regardless of mating order-in almost all contexts; this observed pattern of 'long-sperm precedence' is consistent with female postpostcopulatory choice of high-fitness male traits. Nonetheless, this study also found that this general preference can be plastically altered by females in response to effects including perfuming treatment; this differential female sperm use is between otherwise identical males, and therefore solely female-mediated. Furthermore, this finding that females exercise choice using diverse criteria suggests a possible mechanism for the maintenance of variation in sexually selected male traits. | Rooke, R., Krupp, J. J., Rasool, A., Golemiec, M., Stewart, M., Schneider, J., Levine, J. D. (2024). The gene "degrees of kevin bacon" (dokb) regulates a social network behaviour in Drosophila melanogaster. Nat Commun, 15(1):3339 PubMed ID: 38688961
Summary: Social networks are a mathematical representation of interactions among individuals which are prevalent across various animal species. Studies of human populations have shown the breadth of what can spread throughout a social network: obesity, smoking cessation, happiness, drug use and divorce. 'Betweenness centrality' is a key property of social networks that indicates an individual's importance in facilitating communication and cohesion within the network. Heritability of betweenness centrality has been suggested in several species, however the genetic regulation of this property remains enigmatic. This study demonstrates that the gene CG14109, referred to as degrees of kevin bacon (dokb), influences betweenness centrality in Drosophila melanogaster. Strain-specific alleles of dokb with distinct amino acid sequences and when the dokb allele is exchanged between strains, flies exhibit the betweenness centrality pattern dictated by the donor allele. By inserting a GAL4 reporter into the dokb locus, this study confirmed that dokb is expressed in the central nervous system. These findings define a novel genetic entry point to study social network structure and thereby establish gene-to-social structure relationships. While dokb sequence homology is exclusive to Diptera, it is anticipate that dokb-associated molecular pathways could unveil convergent neural mechanisms of social behaviour that apply in diverse animal species. |
| Peng, D., Zheng, L., Liu, D., Han, C., Wang, X., Yang, Y., Song, L., Zhao, M., Wei, Y., Li, J., Ye, X., Wei, Y., Feng, Z., Huang, X., Chen, M., Gou, Y., Xue, Y., Zhang, L. (2024). Large-language models facilitate discovery of the molecular signatures regulating sleep and activity. Nat Commun, 15(1):3685 PubMed ID: 38693116
Summary: Sleep, locomotor and social activities are essential animal behaviors, but their reciprocal relationships and underlying mechanisms remain poorly understood. This study elicited information from a cutting-edge large-language model (LLM), generative pre-trained transformer (GPT) 3.5, which interprets 10.2-13.8% of Drosophila genes known to regulate the 3 behaviors. An instrument was developed for simultaneous video tracking of multiple moving objects, and a genome-wide screen was conducwte. 758 fly genes were identified that regulate sleep and activities, including mre11 which regulates sleep only in the presence of conspecifics, and NELF-B which regulates sleep regardless of whether conspecifics are present. Based on LLM-reasoning, an educated signal web is modeled for understanding of potential relationships between its components, presenting comprehensive molecular signatures that control sleep, locomotor and social activities. This LLM-aided strategy may also be helpful for addressing other complex scientific questions. | Draper, I. R., Roberts, M. A., Gailloud, M., Jackson, F. R. (2024). Drosophila noktochor regulates night sleep via a local mushroom body circuit. iScience, 27(3):109106 PubMed ID: 38380256
Summary: This study shows that a sleep-regulating, Ig-domain protein (NKT) is secreted from Drosophila mushroom body (MB) α'/β' neurons to act locally on other MB cell types. Pan-neuronal or broad MB expression of membrane-tethered NKT (tNkt) protein reduced sleep, like that of an NKT null mutant, suggesting blockade of a receptor mediating endogenous NKT action. In contrast, expression in neurons requiring NKT (the MB α'/β' cells), or non-MB sleep-regulating centers, did not reduce night sleep, indicating the presence of a local MB sleep-regulating circuit consisting of communicating neural subtypes. It id suggested that the leucocyte-antigen-related like (Lar) transmembrane receptor may mediate NKT action. Knockdown or overexpression of Lar in the MB increased or decreased sleep, respectively, indicating the receptor promotes wakefulness. Surprisingly, selective expression of tNkt or knockdown of Lar in MB wake-promoting cells increased rather than decreased sleep, suggesting that NKT acts on wake- as well as sleep-promoting cell types to regulate sleep. |
Monday January 13th - Chromatin and DNA repaired |
| Koestler, S. A., Ball, M. L., Muresan, L., Dinakaran, V., White, R. (2024). Transcriptionally active chromatin loops contain both 'active' and 'inactive' histone modifications that exhibit exclusivity at the level of nucleosome clusters. Epigenetics & chromatin, 17(1):8 PubMed ID: 38528624
Summary: Chromatin state is thought to impart regulatory function to the underlying DNA sequence. This can be established through histone modifications and chromatin organisation, but exactly how these factors relate to one another to regulate gene expression is unclear. In this study, super-resolution microscopy was used to image the Y loops of Drosophila melanogaster primary spermatocytes, which are enormous transcriptionally active chromatin fibres, each representing single transcription units that are individually resolvable in the nuclear interior. Previously work found that the Y loops consist of regular clusters of nucleosomes, with an estimated median of 54 nucleosomes per cluster with wide variation. This study reports that the histone modifications H3K4me3, H3K27me3, and H3K36me3 are also clustered along the Y loops, with H3K4me3 more associated with diffuse chromatin compared to H3K27me3. These histone modifications form domains that can be stretches of Y loop chromatin micrometres long, or can be in short alternating domains. The different histone modifications are associated with different sizes of chromatin clusters and unique morphologies. Strikingly, a single chromatin cluster almost always only contains only one type of the histone modifications that were labelled, suggesting exclusivity, and therefore regulation at the level of individual chromatin clusters. The active mark H3K36me3 is more associated with actively elongating RNA polymerase II than H3K27me3, with polymerase often appearing on what are assumed to be looping regions on the periphery of chromatin clusters.These results provide a foundation for understanding the relationship between chromatin state, chromatin organisation, and transcription regulation - with potential implications for pause-release dynamics, splicing complex organisation and chromatin dynamics during polymerase progression along a gene. | Kamalyan, S., Kyrchanova, O., Klimenko, N., Babosha, V., Vasileva, Y., Belova, E., Fursenko, D., Maksimenko, O., Georgiev, P. (2024). The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality. Epigenetics & chromatin, 17(1):9 PubMed ID: 38561749
Summary: CTCF is highly likely to be the ancestor of proteins that contain large clusters of C2H2 zinc finger domains, and its conservation is observed across most bilaterian organisms. In mammals, CTCF is the primary architectural protein involved in organizing chromosome topology and mediating enhancer-promoter interactions over long distances. In Drosophila, CTCF (dCTCF) cooperates with other architectural proteins to establish long-range interactions and chromatin boundaries. CTCFs of various organisms contain an unstructured N-terminal dimerization domain (DD) and clusters comprising eleven zinc-finger domains of the C2H2 type. The Drosophila (dCTCF) and human (hCTCF) CTCFs share sequence homology in only five C2H2 domains that specifically bind to a conserved 15 bp motif. Previous work demonstrated that CTCFs from different organisms carry unstructured N-terminal dimerization domains (DDs) that lack sequence homology. This study used the CTCF(attP(mCh)) platform to introduce desired changes in the Drosophila CTCF gene and generated a series of transgenic lines expressing dCTCF with different variants of the N-terminal domain. The findings revealed that the functionality of dCTCF is significantly affected by the deletion of the N-terminal DD. Additionally, a strong impact was observed on the binding of the dCTCF mutant to chromatin upon deletion of the DD. However, chromatin binding was restored in transgenic flies expressing a chimeric CTCF protein with the DD of hCTCF. Although the chimeric protein exhibited lower expression levels than those of the dCTCF variants, it efficiently bound to chromatin similarly to the wild type (wt) protein. These findings suggest that one of the evolutionarily conserved functions of the unstructured N-terminal dimerization domain is to recruit dCTCF to its genomic sites in vivo. |
| Graham, E. L., Fernandez, J., Gandhi, S., Choudhry, I., Kellam, N., LaRocque, J. R. (2024). The impact of developmental stage, tissue type, and sex on DNA double-strand break repair in Drosophila melanogaster. PLoS Genet, 20(4):e1011250 PubMed ID: 38683763
Summary: Accurate repair of DNA double-strand breaks (DSBs) is essential for the maintenance of genome integrity, as failure to repair DSBs can result in cell death. The cell has evolved two main mechanisms for DSB repair: non-homologous end-joining (NHEJ) and homology-directed repair (HDR), which includes single-strand annealing (SSA) and homologous recombination (HR). While certain factors like age and state of the chromatin are known to influence DSB repair pathway choice, the roles of developmental stage, tissue type, and sex have yet to be elucidated in multicellular organisms. To examine the influence of these factors, DSB repair in various embryonic developmental stages, larva, and adult tissues in Drosophila melanogaster was analyzed through molecular analysis of the DR-white assay using Tracking across Indels by DEcomposition (TIDE). The proportion of HR repair was highest in tissues that maintain the canonical (G1/S/G2/M) cell cycle and suppressed in both terminally differentiated and polyploid tissues. To determine the impact of sex on repair pathway choice, repair in different tissues in both males and females was analyzed. When molecularly examining tissues containing mostly somatic cells, males and females demonstrated similar proportions of HR and NHEJ. However, when DSB repair was analyzed in male and female premeiotic germline cells utilizing phenotypic analysis of the DR-white assay, there was a significant decrease in HR in females compared to males. This study describes the impact of development, tissue-specific cycling profile, and, in some cases, sex on DSB repair outcomes, underscoring the complexity of repair in multicellular organisms. | Melnikova, L. S., Molodina, V. V., Georgiev, P. G., Golovnin, A. K. (2024). Role of Mod(mdg4)-67.2 Protein in Interactions between Su(Hw)-Dependent Complexes and Their Recruitment to Chromatin. Biochemistry (Mosc), 89(4):626-636 PubMed ID: 38831500
Summary: Su(Hw) belongs to the class of proteins that organize chromosome architecture, determine promoter activity, and participate in formation of the boundaries/insulators between the regulatory domains. This protein contains a cluster of 12 zinc fingers of the C2H2 type, some of which are responsible for binding to the consensus site. The Su(Hw) protein forms complex with the Mod(mdg4)-67.2 and the CP190 proteins, where the last one binds to all known Drosophila insulators. To further study functioning of the Su(Hw)-dependent complexes, the previously described su(Hw)(E8) mutation was used with inactive seventh zinc finger, which produces mutant protein that cannot bind to the consensus site. The present work shows that the Su(Hw)(E8) protein continues to directly interact with the CP190 and Mod(mdg4)-67.2 proteins. Through interaction with Mod(mdg4)-67.2, the Su(Hw)(E8) protein can be recruited into the Su(Hw)-dependent complexes formed on chromatin and enhance their insulator activity. These results demonstrate that the Su(Hw) dependent complexes without bound DNA can be recruited to the Su(Hw) binding sites through the specific protein-protein interactions that are stabilized by Mod(mdg4)-67.2. |
| Manning, S. A., Kroeger, B., Deng, Q., Brooks, E., Fonseka, Y., Hinde, E., Harvey, K. F. (2024). The Drosophila Hippo pathway transcription factor Scalloped and its co-factors alter each other's chromatin binding dynamics and transcription in vivo. Dev Cell, 59(13):1640-1654. PubMed ID: 38670104
Summary: he Hippo pathway is an important regulator of organ growth and cell fate. The major mechanism by which Hippo is known to control transcription is by dictating the nucleo-cytoplasmic shuttling rate of Yorkie, a transcription co-activator, which promotes transcription with the DNA binding protein Scalloped. The nuclear biophysical behavior of Yorkie and Scalloped, and whether this is regulated by the Hippo pathway, remains unexplored. Using multiple live-imaging modalities on Drosophila tissues, this study found that Scalloped interacts with DNA on a broad range of timescales, and enrichment of Scalloped at sites of active transcription is mediated by longer DNA dwell times. Further, Yorkie increased Scalloped's DNA dwell time, whereas the repressors Nervous fingers 1 (Nerfin-1) and Tondu-domain-containing growth inhibitor (Tgi) decreased it. Therefore, the Hippo pathway influences transcription not only by controlling nuclear abundance of Yorkie but also by modifying the DNA binding kinetics of the transcription factor Scalloped. | Carlson, J., Neidviecky, E., Cook, I., Cross, B., Deng, H. (2024). Interaction with B-type lamin reveals the function of Drosophila Keap1 xenobiotic response factor in nuclear architecture. Molecular biology reports, 51(1):556 PubMed ID: 38642177
Summary: The |
Friday January 10th - Larval and Adult Development |
| Turingan, M. J., Li, T., Wright, J., Sharma, A., Ding, K., Khan, S., Lee, B., Grewal, S. S. (2024). Hypoxia delays steroid-induced developmental maturation in Drosophila by suppressing EGF signaling. PLoS Genet, 20(4):e1011232 PubMed ID: 38669270
Summary: Animals often grow and develop in unpredictable environments where factors like food availability, temperature, and oxygen levels can fluctuate dramatically. To ensure proper sexual maturation into adulthood, juvenile animals need to adapt their growth and developmental rates to these fluctuating environmental conditions. Failure to do so can result in impaired maturation and incorrect body size. This study describes a mechanism by which Drosophila larvae adapt their development in low oxygen (hypoxia). During normal development, larvae grow and increase in mass until they reach critical weight (CW), after which point a neuroendocrine circuit triggers the production of the steroid hormone ecdysone from the prothoracic gland (PG), which promotes maturation to the pupal stage. However, when raised in hypoxia (5% oxygen), larvae slow their growth and delay their maturation to the pupal stage. Although hypoxia delays the attainment of CW, the maturation delay occurs mainly because of hypoxia acting late in development to suppress ecdysone production. This suppression operates through a distinct mechanism from nutrient deprivation, occurs independently of HIF-1 alpha and does not involve dilp8 or modulation of Ptth, the main neuropeptide that initiates ecdysone production in the PG. Instead, this study found that hypoxia lowers the expression of the EGF ligand, Spitz, and that the delay in maturation occurs due to reduced EGFR/ERK signaling in the PG. This study sheds light on how animals can adjust their development rate in response to changing oxygen levels in their environment. Given that hypoxia is a feature of both normal physiology and many diseases, these findings have important implications for understanding how low oxygen levels may impact animal development in both normal and pathological situations. | Beno, M., Benova-Liszekova, D., Kostic, I., Sery, M., Mentelova, L., Prochazka, M., Soltys, J., Trusinova, L., Ritomsky, M., Orovcik, L., Jerigova, M., Velic, D., Machata, P., Omastova, M., Chase, B. A., Farkas, R. (2024). Gross morphology and adhesion-associated physical properties of Drosophila larval salivary gland glue secretion. Sci Rep, 14(1):9779 PubMed ID: 38684688
Summary: One of the major functions of the larval salivary glands (SGs) of many Drosophila species is to produce a massive secretion during puparium formation. This so-called proteinaceous glue is exocytosed into the centrally located lumen, and subsequently expectorated, serving as an adhesive to attach the puparial case to a solid substrate during metamorphosis. Although this was first described almost 70 years ago, a detailed description of the morphology and mechanical properties of the glue is largely missing. Its main known physical property is that it is released as a watery liquid that quickly hardens into a solid cement. This study provides a detailed morphological and topological analysis of the solidified glue. It forms a distinctive enamel-like plaque that is composed of a central fingerprint surrounded by a cascade of laterally layered terraces. The solidifying glue rapidly produces crystals of KCl on these alluvial-like terraces. Since the properties of the glue affect the adhesion of the puparium to its substrate, and so can influence the success of metamorphosis, this study evaluated over 80 different materials for their ability to adhere to the glue to determine which properties favor strong adhesion. The alkaline Sgs-glue was found to adhere strongly to wettable and positively charged surfaces but not to neutral or negatively charged and hydrophobic surfaces. Puparia formed on unfavored materials can be removed easily without leaving fingerprints or cascading terraces. For successful adhesion of the Sgs-glue, the material surface must display a specific type of triboelectric charge. Interestingly, the expectorated glue can move upwards against gravity on the surface of freshly formed puparia via specific, unique and novel anatomical structures present in the puparial's lateral abdominal segments that as been named bidentia. |
| Puli, O. R., Gogia, N., Chimata, A. V., Yorimitsu, T., Nakagoshi, H., Kango-Singh, M., Singh, A. (2024). Genetic mechanism regulating diversity in the placement of eyes on the head of animals. Proc Natl Acad Sci U S A, 121(16):e2316244121 PubMed ID: 38588419
Summary: Despite the conservation of genetic machinery involved in eye development, there is a strong diversity in the placement of eyes on the head of animals. Morphogen gradients of signaling molecules are vital to patterning cues. During Drosophila eye development, Wingless (Wg), a ligand of Wnt/Wg signaling, is expressed anterolaterally to form a morphogen gradient to determine the eye- versus head-specific cell fate. The underlying mechanisms that regulate this process are yet to be fully understood. defective proventriculus (dve) (Drosophila ortholog of human SATB1), a K50 homeodomain transcription factor, was characterized as a dorsal eye gene, which regulates Wg signaling to determine eye versus head fate. Across Drosophila species, Dve is expressed in the dorsal head vertex region where it regulates wg transcription. Second, Dve suppresses eye fate by down-regulating retinal determination genes. Third, the dve-expressing dorsal head vertex region is important for Wg-mediated inhibition of retinal cell fate, as eliminating the Dve-expressing cells or preventing Wg transport from these dve-expressing cells leads to a dramatic expansion of the eye field. Together, these findings suggest that Dve regulates Wg expression in the dorsal head vertex, which is critical for determining eye versus head fate. Gain-of-function of SATB1 exhibits an eye fate suppression phenotype similar to Dve. These data demonstrate a conserved role for Dve/SATB1 in the positioning of eyes on the head and the interocular distance by regulating Wg. This study provides evidence that dysregulation of the Wg morphogen gradient results in developmental defects such as hypertelorism in humans where disproportionate interocular distance and facial anomalies are reported. | Mehaffey, T. M., Hecht, C. A., White, J. S., Hutson, M. S., Page-McCaw, A. (2024). Live imaging basement membrane assembly under the pupal notum epithelium. microPublication biology. PubMed ID: 38525127
Summary: Basement membranes are sheet-like extracellular matrices containing Collagen IV, and they are conserved across the animal kingdom. Basement membranes usually line the basal surfaces of epithelia, where they contribute to structure, maintenance, and signaling. Although adult epithelia contact basement membranes, in early embryos the epithelia contact basement membranes only after basement membranes are assembled in embryogenesis. In Drosophila , the pupal notum epithelium is a useful model for live imaging epithelial cell behaviors, yet it is unclear when the basement membrane assembles in the pupa, as pupae are undergoing metamorphosis, similar to embryogenesis. To characterize the basement membrane in the pupal notum, spinning disk fluorescent microscopy was used to visualize Collagen IV subunit Vkg-GFP and adherens junction protein p120ctnRFP. Bright punctae of Vkg-GFP were observed in the X-Y plane, possibly representing Vkg-containing cells. A thin continuous Vkg-containing basement membrane was evident at 14 h APF, which became more enriched with Vkg-GFP over the next 6 h, indicating the basement membrane is still assembling during that time. Live imaging of the pupal notum during this time could provide insight into formation, assembly, and repair of the basement membranes. |
| Krejcva, G., Danielovq, A., Sehadovq, H., Dydka, F., Kubasek, J., Moos, M., Bajgar, A. (2024). Macrophages play a nutritive role in post-metamorphic maturation in Drosophila. Development, 151(7) PubMed ID: 38456486
Summary: In the body of multicellular organisms, macrophages play an indispensable role in maintaining tissue homeostasis by removing old, apoptotic and damaged cells. In addition, macrophages allow significant remodeling of body plans during embryonic morphogenesis, regeneration and metamorphosis. Although the huge amount of organic matter that must be removed during these processes represents a potential source of nutrients, their further use by the organism has not yet been addressed. This study documented that, during metamorphosis, Drosophila larval adipose tissue is infiltrated by macrophages, which remove dying adipocytes by efferocytosis and engulf leaking RNA-protein granules and lipids. Consequently, the infiltrating macrophages transiently adopt the adipocyte-like metabolic profile to convert remnants of dying adipocytes to lipoproteins and storage peptides that nutritionally support post-metamorphic development. This process is fundamental for the full maturation of ovaries and the achievement of early fecundity of individuals. Whether macrophages play an analogous role in other situations of apoptotic cell removal remains to be elucidated. | Sun, X., Decker, J., Sanchez-Luege, N., Rebay, I. (2024). Inter-plane feedback coordinates cell morphogenesis and maintains 3D tissue organization in the Drosophila pupal retina. Development, 151(6) PubMed ID: 38533736
Summary: How complex organs coordinate cellular morphogenetic events to achieve three-dimensional (3D) form is a central question in development. The question is uniquely tractable in the late Drosophila pupal retina, where cells maintain stereotyped contacts as they elaborate the specialized cytoskeletal structures that pattern the apical, basal and longitudinal planes of the epithelium. This study combined cell type-specific genetic manipulation of the cytoskeletal regulator Abelson (Abl) with 3D imaging to explore how the distinct cellular morphogenetic programs of photoreceptors and interommatidial pigment cells (IOPCs) organize tissue pattern to support retinal integrity. These experiments show that photoreceptor and IOPC terminal differentiation is unexpectedly interdependent, connected by an intercellular feedback mechanism that coordinates and promotes morphogenetic change across orthogonal tissue planes to ensure correct 3D retinal pattern. It is proposed that genetic regulation of specialized cellular differentiation programs combined with inter-plane mechanical feedback confers spatial coordination to achieve robust 3D tissue morphogenesis. |
Wednesday January 8th - Evolution |
| Liu, J., Zheng, C., Duan, Y. (2024). New comparative genomic evidence supporting the proteomic diversification role of A-to-I RNA editing in insects. Mol Genet Genomics, 299(1):46 PubMed ID: 38642133
Summary: Adenosine-to-inosine (A-to-I) RNA editing, resembling A-to-G mutation, confers adaptiveness by increasing proteomic diversity in a temporal-spatial manner. This evolutionary theory named "proteomic diversifying hypothesis" has only partially been tested in very few organisms like Drosophila melanogaster, mainly by observing the positive selection on nonsynonymous editing events. To find additional genome-wide evidences supporting this interesting assumption, this study retrieved the genomes of four Drosophila species and collected 20 deep-sequenced transcriptomes of different developmental stages and neuron populations of D. melanogaster. The RNA editomes in these samples was systematically profiled and meticulous comparative genomic analyses was performed. Further evidences were found to support the diversifying hypothesis. (1) None of the nonsynonymous editing sites in D. melanogaster had ancestral G-alleles, while the silent editing sites had an unignorable fraction of ancestral G-alleles; (2) Only very few nonsynonymous editing sites in D. melanogaster had corresponding G-alleles derived in the genomes of sibling species, and the fraction of such situation was significantly lower than that of silent editing sites; (3) The few nonsynonymous editing with corresponding G-alleles had significantly more variable editing levels (across samples) than other nonsynonymous editing sites in D. melanogaster. The proteomic diversifying nature of RNA editing in Drosophila excludes the restorative role which favors an ancestral G-allele. The few fixed G-alleles in sibling species might facilitate the adaptation to particular environment and the corresponding nonsynonymous editing in D. melanogaster would introduce stronger advantage of flexible proteomic diversification. With multi-Omics data, this study consolidates the nature of evolutionary significance of A-to-I RNA editing sites in model insects. | De Lisle, S. P. (2024). Genotype-Environment interaction and the evolution of sexual dimorphism: adult nutritional environment mediates selection and expression of sex-specific genetic variance in Drosophila melanogaster. J Evol Biol, 37(7):770-778 PubMed ID: 38668688
Summary: Sexual conflict plays a key role in the dynamics of adaptive evolution in sexually reproducing populations, and theory suggests an important role for variance in resource acquisition in generating or masking sexual conflict over fitness and life history traits. This study used a quantitative genetic genotype-environment experiment in Drosophila melanogaster to test the theoretical prediction that variance in resource acquisition mediates variation in sex-specific component fitness. Holding larval conditions constant, this study found that adult nutritional environments characterized by high protein content resulted in reduced survival of both sexes and lower male reproductive success compared to an environment of lower protein content. Despite reduced mean fitness of both sexes in high protein environments, a sex*treatment interaction was found for the relationship between resource acquisition and fitness; estimates of the adaptive landscape indicate males were furthest from their optimum resource acquisition level in high protein environments, and females were furthest in low protein environments. Expression of genetic variance in resource acquisition and survival was highest for each sex in the environment it was best adapted to, although the treatment effects on expression of genetic variance eroded in the path from resource acquisition to total fitness. Cross-sex genetic correlations were strongly positive for resource acquisition, survival, and total fitness and negative for mating success, although estimation error was high for all. These results demonstrate that environmental effects on resource acquisition can have predictable consequences for the expression of sex-specific genetic variance but also that these effects of resource acquisition can erode through life history. |
| 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. Curr Biol, 34(11):2319-2329.e2316 PubMed ID: 38688283
Summary: How evolutionary changes in genes and neurons encode species variation in complex motor behaviors is 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, which 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 supporting the sine circuit connectivity. Optogenetic activation confirms that TN1 neurons in D. yakuba have lost the ability to drive sine song, although they have maintained 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. | Scarpa, A., Pianezza, R., Wierzbicki, F., Kofler, R. (2024). Genomes of historical specimens reveal multiple invasions of LTR retrotransposons in Drosophila melanogaster during the 19th century. Proc Natl Acad Sci U S A, 121(15):e2313866121 PubMed ID: 38564639
Summary: Transposable element invasions have a profound impact on the evolution of genomes and phenotypes. It is thus an important open question how often such TE invasions occur. To address this question, the genomes of historical specimens, sampled about 200 y ago were used. The LTR retrotransposons Blood, Opus, and 412 were shown to spread in Drosophila melanogaster in the 19th century. These invasions constitute second waves, as degraded fragments were found for all three TEs. The composition of Opus and 412, but not of Blood, shows a pronounced geographic heterogeneity, likely due to founder effects during the invasions. Finally, species from the Drosophila simulans complex were identified as the likely origin of the TEs. In total, seven TE families invaded D. melanogaster during the last 200y, thereby increasing the genome size by up to 1.2Mbp. It is suggested that this high rate of TE invasions was likely triggered by human activity. Based on the analysis of strains and specimens sampled at different times, this study provides a detailed timeline of TE invasions, making D. melanogaster the first organism where the invasion history of TEs during the last two centuries could be inferred. |
| Tian, S., Asano, Y., Banerjee, T. D., Wee, J. L. Q., Lamb, A., Wang, Y., Murugesan, S. N., Ui-Tei, K., Wittkopp, P. J., Monteiro, A. (2024). A micro-RNA is the effector gene of a classic evolutionary hotspot locus. bioRxiv, PubMed ID: 38659873
Summary: In Lepidoptera (butterflies and moths), the genomic region around the gene cortex is a 'hotspot' locus, repeatedly used to generate intraspecific melanic wing color polymorphisms across 100-million-years of evolution. However, the identity of the effector gene regulating melanic wing color within this locus remains unknown. This study shows that none of the four candidate protein-coding genes within this locus, including cortex, serve as major effectors. Instead, a micro-RNA (miRNA), mir-193, serves as the major effector across three deeply diverged lineages of butterflies, and its function is conserved in Drosophila. In Lepidoptera, mir-193 is derived from a gigantic long non-coding RNA, ivory, and it functions by directly repressing multiple pigmentation genes. This study shows that a miRNA can drive repeated instances of adaptive evolution in animals. | Cao, J., Luo, Y., Chen, Y., Wu, Z., Zhang, J., Wu, Y., Hu, W. (2024). Maternal mitochondrial function affects paternal mitochondrial inheritance in Drosophila. Genetics, 226(4) PubMed ID: 38290047
Summary: The maternal inheritance of mitochondria is a widely accepted paradigm, and mechanisms that prevent paternal mitochondria transmission to offspring during spermatogenesis and postfertilization have been described. Although certain species do retain paternal mitochondria, the factors affecting paternal mitochondria inheritance in these cases are unclear. More importantly, the evolutionary benefit of retaining paternal mitochondria and their ultimate fate are unknown. This study shows that transplanted exogenous paternal D. yakuba mitochondria can be transmitted to offspring when maternal mitochondria are dysfunctional in D. melanogaster. Furthermore, the preserved paternal mitochondria are shown to be functional, and can be stably inherited, such that the proportion of paternal mitochondria increases gradually in subsequent generations. This work has important implications that paternal mitochondria inheritance should not be overlooked as a genetic phenomenon in evolution, especially when paternal mitochondria are of significant differences from the maternal mitochondria or the maternal mitochondria are functionally abnormal. These results improve the understanding of mitochondrial inheritance and provide a new model system for its study. |
Tuesday January 7th - Adult Physiology and Metabolism |
| Poidevin, M., Mazuras, N., Bontonou, G., Delamotte, P., Denis, B., Devilliers, M., Akiki, P., Petit, D., de Luca, L., Soulie, P., Gillet, C., Wicker-Thomas, C., Montagne, J. (2024). A fatty acid anabolic pathway in specialized-cells sustains a remote signal that controls egg activation in Drosophila. PLoS Genet, 20(3):e1011186 PubMed ID: 38483976
Summary: Egg activation, representing the critical oocyte-to-embryo transition, provokes meiosis completion, modification of the vitelline membrane to prevent polyspermy, and translation of maternally provided mRNAs. This transition is triggered by a calcium signal induced by spermatozoon fertilization in most animal species, but not in insects. In Drosophila melanogaster, mature oocytes remain arrested at metaphase-I of meiosis and the calcium-dependent activation occurs while the oocyte moves through the genital tract. This study discovered that the oenocytes of fruitfly females are required for egg activation. Oenocytes, cells specialized in lipid-metabolism, are located beneath the abdominal cuticle. In adult flies, they synthesize the fatty acids (FAs) that are the precursors of cuticular hydrocarbons (CHCs), including pheromones. The oenocyte-targeted knockdown of a set of FA-anabolic enzymes, involved in very-long-chain fatty acid (VLCFA) synthesis, leads to a defect in egg activation. Given that some but not all of the identified enzymes are required for CHC/pheromone biogenesis, this putative VLCFA-dependent remote control may rely on an as-yet unidentified CHC or may function in parallel to CHC biogenesis. Additionally, it was discovered that the most posterior ventral oenocyte cluster is in close proximity to the uterus. Since oocytes dissected from females deficient in this FA-anabolic pathway can be activated in vitro, this regulatory loop likely operates upstream of the calcium trigger. These findings provide the first evidence that a physiological extra-genital signal remotely controls egg activation. Moreover, this study highlights a potential metabolic link between pheromone-mediated partner recognition and egg activation. | Moon, S. J., Hu, Y., Dzieciatkowska, M., Kim, A. R., Chen, P. L., Asara, J. M., D'Alessandro, A., Perrimon, N. (2024). Identification of high sugar diet-induced dysregulated metabolic pathways in muscle using tissue-specific metabolic models in Drosophila. bioRxiv, PubMed ID: 38712132
Summary: Individual tissues perform highly specialized metabolic functions to maintain whole-body homeostasis. Although Drosophila serves as a powerful model for studying human metabolic diseases, a lack of tissue-specific metabolic models makes it challenging to quantitatively assess the metabolic processes of individual tissues and disease models in this organism. To address this issue, 32 tissue-specific genome-scale metabolic models (GEMs) were constructed using pseudo-bulk single cell transcriptomics data, revealing distinct metabolic network structures were predicted across tissues. Leveraging enzyme kinetics and flux analyses, ]tissue-dependent metabolic pathway activities, recapitulating known tissue functions and identifying tissue-specific metabolic signatures, as supported by metabolite profiling. Moreover, to demonstrate the utility of tissue-specific GEMs in a disease context, the effect of a high sugar diet (HSD) on muscle metabolism. Together with (13)C-glucose isotopic tracer studies, glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was examined as a rate-limiting enzyme in response to HSD. Mechanistically, the decreased GAPDH activity was linked to elevated NADH/NAD(+) ratio, caused by disturbed NAD(+) regeneration rates, and oxidation of GAPDH. Furthermore, a pathway flux index was introduced to predict and validate additionally perturbed pathways, including fructose and butanoate metabolism. Altogether, these results represent a significant advance in generating quantitative tissue-specific GEMs and flux analyses in Drosophila, highlighting their use for identifying dysregulated metabolic pathways and their regulation in a human disease model. |
| 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, 79(4) PubMed ID: 38198696
Summary: 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 3 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. Additionally, the expression of key regulators involved in mitochondrial dynamics and biogenic signaling pathways was examined. 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, and peroxisome proliferator-activated receptor-γ coactivator-1α. Therefore, the practice of Yo-yo dieting extends the lifespan of fruit flies by modulating mitochondrial dynamics and the associated biogenic signaling pathways. | Wesseltoft, J. B., Danielsen, C. D., Andersen, A. M., de Jonge, N., Olsen, A., Rohde, P. D., Kristensen, T. N. (2024). Feeding Drosophila gut microbiomes from young and old flies modifies the microbiome. Sci Rep, 14(1):7799 PubMed ID: 38565609
Summary: It is becoming increasingly evident that the myriad of microbes in the gut, within cells and attached to body parts (or roots of plants), play crucial roles for the host. Although this has been known for decades, recent developments in molecular biology allow for expanded insight into the abundance and function of these microbes. This study used the vinegar fly, Drosophila melanogaster, to investigate fitness measures across the lifetime of flies fed a suspension of gut microbes harvested from young or old flies, respectively. It was hypothesized that flies constitutively enriched with a 'Young microbiome' would live longer and be more agile at old age (i.e. have increased healthspan) compared to flies enriched with an 'Old microbiome'. Three major take home messages came out of this study: (1) the gut microbiomes of young and old flies differ markedly; (2) feeding flies with Young and Old microbiomes altered the microbiome of recipient flies and (3) the two different microbial diets did not have any effect on locomotor activity nor lifespan of the recipient flies, contradicting the working hypothesis. Combined, these results provide novel insight into the interplay between hosts and their microbiomes and clearly highlight that the phenotypic effects of gut transplants and probiotics can be complex and unpredictable. |
| Yin, J., Chen, H. L., Grigsby-Brown, A., He, Y., Cotten, M. L., Short, J., Dermady, A., Lei, J., Gibbs, M., Cheng, E. S., Zhang, D., Long, C., Xu, L., Zhong, T., Abzalimov, R., Haider, M., Sun, R., He, Y., Zhou, Q., Tjandra, N., Yuan, Q. (2024). Glia-derived secretory fatty acid binding protein Obp44a regulates lipid storage and efflux in the developing Drosophila brain. bioRxiv, PubMed ID: 38645138
Summary: Glia derived secretory factors play diverse roles in supporting the development, physiology, and stress responses of the central nervous system (CNS). Through transcriptomics and imaging analyses, this study has identified Obp44a as one of the most abundantly produced secretory proteins from Drosophila CNS glia. Protein structure homology modeling and Nuclear Magnetic Resonance (NMR) experiments reveal Obp44a as a fatty acid binding protein (FABP) with a high affinity towards long-chain fatty acids in both native and oxidized forms. Further analyses demonstrate that Obp44a effectively infiltrates the neuropil, traffics between neuron and glia, and is secreted into hemolymph, acting as a lipid chaperone and scavenger to regulate lipid and redox homeostasis in the developing brain. In agreement with this essential role, deficiency of Obp44a leads to anatomical and behavioral deficits in adult animals and elevated oxidized lipid levels. Collectively, these findings unveil the crucial involvement of a noncanonical lipid chaperone to shuttle fatty acids within and outside the brain, as needed to maintain a healthy brain lipid environment. These findings could inspire the design of novel approaches to restore lipid homeostasis that is dysregulated in CNS diseases. | Haynes, P. R., Pyfrom, E. S., Li, Y., Stein, C., Cuddapah, V. A., Jacobs, J. A., Yue, Z., Sehgal, A. (2024). A neuron-glia lipid metabolic cycle couples daily sleep to mitochondrial homeostasis.Nat Neurosci, 27(4):666-678 PubMed ID: 38360946
Summary: Sleep is thought to be restorative to brain energy homeostasis, but it is not clear how this is achieved. This study shows that Drosophila glia exhibit a daily cycle of glial mitochondrial oxidation and lipid accumulation that is dependent on prior wake and requires the Drosophila APOE orthologs NLaz and GLaz, which mediate neuron-glia lipid transfer. In turn, a full night of sleep is required for glial lipid clearance, mitochondrial oxidative recovery and maximal neuronal mitophagy. Knockdown of neuronal NLaz causes oxidative stress to accumulate in neurons, and the neuronal mitochondrial integrity protein, Drp1, is required for daily glial lipid accumulation. These data suggest that neurons avoid accumulation of oxidative mitochondrial damage during wake by using mitophagy and passing damage to glia in the form of lipids. mitochondrial lipid metabolic cycle between neurons and glia was proposed to reflect a fundamental function of sleep relevant for brain energy homeostasis. |
Monday January 6th - Adult neural development, structure and function |
| Mao, R., Yu, J., Deng, B., Dai, X., Du, Y., Du, S., Zhang, W., Rao, Y. (2024). Conditional chemoconnectomics (cCCTomics) as a strategy for efficient and conditional targeting of chemical transmission. Elife, 12 PubMed ID: 38686992
Summary: Dissection of neural circuitry underlying behaviors is a central theme in neurobiology. The concept of chemoconnectome (CCT) was previously proposed to cover the entire chemical transmission between neurons and target cells in an organism and created tools for studying it (CCTomics) by targeting all genes related to the CCT in Drosophila. This study has created lines targeting the CCT in a conditional manner after modifying GFP RNA interference, Flp-out, and CRISPR/Cas9 technologies. All three strategies have been validated to be highly effective, with the best using chromatin-peptide fused Cas9 variants and scaffold optimized sgRNAs. As a proof of principle, a comprehensive intersection analysis of CCT genes expression profiles in the clock neurons, uncovering 43 CCT genes present in clock neurons. Specific elimination of each from clock neurons revealed that loss of the neuropeptide CNMamide (CNMa) in two posterior dorsal clock neurons (DN1ps) or its receptor (CNMaR) caused advanced morning activity, indicating a suppressive role of CNMa-CNMaR on morning anticipation, opposite to the promoting role of PDF-PDFR on morning anticipation. These results demonstrate the effectiveness of conditional CCTomics and its tools created here and establish an antagonistic relationship between CNMa-CNMaR and PDF-PDFR signaling in regulating morning anticipation. | Shang, X., Talross, G. J. S., Carlson, J. R. (2024). Exitron splicing of odor receptor genes in Drosophila. Proc Natl Acad Sci U S A, 121(13):e2320277121 PubMed ID: 38507450
Summary: Proper expression of odor receptor genes is critical for the function of olfactory systems. This study identified exitrons (exonic introns) in four of the 39 Odorant receptor (Or) genes expressed in the Drosophila antenna. Exitrons are sequences that can be spliced out from within a protein-coding exon, thereby altering the encoded protein. This study focused on Or88a, which encodes a pheromone receptor and found that exitron splicing of Or88a is conserved across five Drosophila species over 20 My of evolution. The exitron was spliced out in 15% of Or88a transcripts. Removal of this exitron creates a non-coding RNA rather than an RNA that encodes a stable protein. These results suggest the hypothesis that in the case of Or88a, exitron splicing could act in neuronal modulation by decreasing the level of functional Or transcripts. Activation of Or88a-expressing olfactory receptor neurons via either optogenetics or pheromone stimulation increased the level of exitron-spliced transcripts, with optogenetic activation leading to a 14-fold increase. A fifth Or can also undergo an alternative splicing event that eliminates most of the canonical open reading frame. Besides these cases of alternative splicing, alternative polyadenylation of four Ors and exposure of Or67c to its ligand ethyl lactate in the antenna downregulated all of its 3' isoforms. This study reveals mechanisms by which neuronal activity could be modulated via regulation of the levels of Or isoforms. |
| Singh, B. N., Tran, H., Kramer, J., Kirichenko, E., Changela, N., Wang, F., Feng, Y., Kumar, D., Tu, M., Lan, J., Bizet, M., Fuks, F., Steward, R. (2024). Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates axon guidance genes in Drosophila. PLoS One, 19(2):e0293894 PubMed ID: 38381741
Summary: Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases and catalyze the transition of 5mC to 5hmC in DNA. These enzymes have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila as Tet knock-out animals do not reach adulthood. The identification is described of Tet-target genes in the embryo and larval brain by mapping one, Tet DNA-binding sites throughout the genome and two, the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC modifications are distributed along the entire transcript, while Tet DNA-binding sites are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are preferentially involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. These results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs primarily in cells of the nervous system. | Yu, H., Liu, D., Zhang, Y., Tang, R., Fan, X., Mao, S., Lv, L., Chen, F., Qin, H., Zhang, Z., van Aalten, D. M. F., Yang, B., Yuan, K. (2024). Tissue-specific O-GlcNAcylation profiling identifies substrates in translational machinery in Drosophila mushroom body contributing to olfactory learning. Elife, 13 PubMed ID: 38619103
Summary: O-GlcNAcylation is a dynamic post-translational modification that diversifies the proteome. Its dysregulation is associated with neurological disorders that impair cognitive function, and yet identification of phenotype-relevant candidate substrates in a brain-region specific manner remains unfeasible. By combining an O-GlcNAc binding activity derived from Clostridium perfringens OGA (CpOGA) with TurboID proximity labeling in Drosophila, this study developed an O-GlcNAcylation profiling tool that translates O-GlcNAc modification into biotin conjugation for tissue-specific candidate substrates enrichment. The O-GlcNAc interactome in major brain regions of Drosophila was mapped, and components of the translational machinery, particularly ribosomal subunits, were found to be abundantly O-GlcNAcylated in the mushroom body of Drosophila brain. Hypo-O-GlcNAcylation induced by ectopic expression of active CpOGA in the mushroom body decreased local translational activity, leading to olfactory learning deficits that could be rescued by dMyc overexpression-induced increase of protein synthesis. This study provides a useful tool for future dissection of tissue-specific functions of O-GlcNAcylation in Drosophila, and suggests a possibility that O-GlcNAcylation impacts cognitive function via regulating regional translational activity in the brain. |
| Bence, M., Jankovics, F., Kristo, I., Gyetvai, A., Vertessy, B. G., Erdelyi, M. (2024). Direct interaction of Su(var)2-10 via the SIM-binding site of the Piwi protein is required for transposon silencing in Drosophila melanogaster. Febs j, 291(8):1759-1779 PubMed ID: 38308815
Summary: Nuclear Piwi/Piwi-interacting RNA complexes mediate co-transcriptional silencing of transposable elements by inducing local heterochromatin formation. In Drosophila, sumoylation plays an essential role in the assembly of the silencing complex; however, the molecular mechanism by which the sumoylation machinery is recruited to the transposon loci is poorly understood. This study shows that the Drosophila E3 SUMO-ligase Su(var)2-10 directly binds to the Piwi protein. This interaction is mediated by the SUMO-interacting motif-like (SIM-like) structure in the C-terminal domain of Su(var)2-10. The SIM-like structure was demonstrated to bind to a special region found in the MID domain of the Piwi protein, the structure of which is highly similar to the SIM-binding pocket of SUMO proteins. Abrogation of the Su(var)2-10-binding surface of the Piwi protein resulted in transposon derepression in the ovary of adult flies. Based on these results, a model is proposed in which the Piwi protein initiates local sumoylation in the silencing complex by recruiting Su(var)2-10 to the transposon loci. | Eichler, K., Hampel, S., Alejandro-GarcIa, A., Calle-Schuler, S. A., Santana-Cruz, A., Kmecova, L., Blagburn, J. M., Hoopfer, E. D., Seeds, A. M. (2024). Somatotopic organization among parallel sensory pathways that promote a grooming sequence in Drosophila. Elife, 12 PubMed ID: 38634460
Summary: Mechanosensory neurons located across the body surface respond to tactile stimuli and elicit diverse behavioral responses, from relatively simple stimulus location-aimed movements to complex movement sequences. How mechanosensory neurons and their postsynaptic circuits influence such diverse behaviors remains unclear. It was previously discovered that Drosophila perform a body location-prioritized grooming sequence when mechanosensory neurons at different locations on the head and body are simultaneously stimulated by dust. This study identified nearly all mechanosensory neurons on the Drosophila head that individually elicit aimed grooming of specific head locations, while collectively eliciting a whole head grooming sequence. Different tracing methods were used to reconstruct the projections of these neurons from different locations on the head to their distinct arborizations in the brain. This provides the first synaptic resolution somatotopic map of a head, and defines the parallel-projecting mechanosensory pathways that elicit head grooming. |
Friday January 2nd - Cytoskeleton |
| Jackson, J. A., Denk-Lobnig, M., Kitzinger, K. A., Martin, A. C. (2024). Change in RhoGAP and RhoGEF availability drives transitions in cortical patterning and excitability in Drosophila. Curr Biol, 34(10):2132-2146.e2135 PubMed ID: 38688282
Summary: Actin cortex patterning and dynamics are critical for cell shape changes. These dynamics undergo transitions during development, often accompanying changes in collective cell behavior. Although mechanisms have been established for individual cells' dynamic behaviors, the mechanisms and specific molecules that result in developmental transitions in vivo are still poorly understood. This study took advantage of two developmental systems in Drosophila melanogaster to identify conditions that altered cortical patterning and dynamics. A Rho guanine nucleotide exchange factor (RhoGEF) and Rho GTPase activating protein (RhoGAP) pair required for actomyosin waves in egg chambers. Specifically, depletion of the RhoGEF, Ect2, or the RhoGAP, RhoGAP15B, disrupted actomyosin wave induction, and both proteins relocalized from the nucleus to the cortex preceding wave formation. Furthermore, overexpression of a different RhoGEF and RhoGAP pair, RhoGEF2 and Cumberland gap (C-GAP or Rho GTPase activating protein at 71E), was found to result in actomyosin waves in the early embryo, during which RhoA activation precedes actomyosin assembly by ~4 s. C-GAP was recruited to actomyosin waves, and disrupting F-actin polymerization altered the spatial organization of both RhoA signaling and the cytoskeleton in waves. In addition, disrupting F-actin dynamics increased wave period and width, consistent with a possible role for F-actin in promoting delayed negative feedback. Overall, this study showed a mechanism involved in inducing actomyosin waves that is essential for oocyte development and is general to other cell types, such as epithelial and syncytial cells. | Okenve-Ramos, P., Gosling, R., Chojnowska-Monga, M., Gupta, K., Shields, S., Alhadyian, H., Collie, C., Gregory, E., Sanchez-Soriano, N. (2024). Neuronal ageing is promoted by the decay of the microtubule cytoskeleton. PLoS Biol, 22(3):e3002504 PubMed ID: 38478582
Summary: Natural ageing is accompanied by a decline in motor, sensory, and cognitive functions, all impacting quality of life. Ageing is also the predominant risk factor for many neurodegenerative diseases, including Parkinson's disease and Alzheimer's disease. It is therefore necessary to gain a better understanding of the cellular and physiological processes underlying age-related neuronal decay. However, gaining this understanding is a slow process due to the large amount of time required to age mammalian or vertebrate animal models. This study introduces a new cellular model within the Drosophila brain, in which classical ageing hallmarks previously observed in the primate brain appear. These hallmarks include axonal swellings, cytoskeletal decay, a reduction in axonal calibre, and morphological changes arising at synaptic terminals. In the fly brain, these changes begin to occur within a few weeks, ideal to study the underlying mechanisms of ageing. The decay of the neuronal microtubule (MT) cytoskeleton was shown to precede the onset of other ageing hallmarks. The MT-binding factors Tau, EB1, and Shot/MACF1, are necessary for MT maintenance in axons and synapses, and their functional loss during ageing triggers MT bundle decay, followed by a decline in axons and synaptic terminals. Furthermore, genetic manipulations that improve MT networks slowed down the onset of neuronal ageing hallmarks and confer aged specimens the ability to outperform age-matched controls. Our work suggests that MT networks are a key lesion site in ageing neurons and therefore the MT cytoskeleton offers a promising target to improve neuronal decay in advanced age. |
| Gu, L., Sauceda, R., Brar, J., Fessahaye, F., Joo, M., Lee, J., Nguyan, J., Teng, M., Weng, M. (2024). A novel protein Moat prevents ectopic epithelial folding by limiting Bazooka/Par3-dependent adherens junctions. bioRxiv, PubMed ID: 38496457
Summary: Cortical myosin contraction and cell adhesion work together to promote tissue shape changes, but how they are modulated to achieve diverse morphogenetic outcomes remains unclear. Epithelial folding occurs via apical constriction, mediated by apical accumulation of contractile myosin engaged with adherens junctions, as in Drosophila ventral furrow formation. While levels of contractile myosin correlate with apical constriction, whether levels of adherens junctions modulate apical constriction is unknown. This study identified a novel Drosophila gene moat that maintains low levels of Bazooka/Par3-dependent adherens junctions and thereby restricts apical constriction to ventral furrow cells with high-level contractile myosin. In moat mutants, abnormally high levels of Bazooka/Par3-dependent adherens junctions promote ectopic apical constriction in cells with low-level contractile myosin, insufficient for apical constriction in wild type. Such ectopic apical constriction expands infolding behavior from ventral furrow to ectodermal anterior midgut, which normally forms a later circular invagination. In moat mutant ventral furrow, a perturbed apical constriction gradient delays infolding. These results indicate that levels of adherens junctions can modulate the outcome of apical constriction, providing an additional mechanism to define morphogenetic boundaries. | McParland, E. D., Butcher, T. A., Gurley, N. J., Johnson, R. I., Slep, K. C., Peifer, M. (2024). The Dilute domain in Canoe is not essential for linking cell junctions to the cytoskeleton but supports morphogenesis robustness. J Cell Sci, 137(6) PubMed ID: 38323935
Summary: Robust linkage between adherens junctions and the actomyosin cytoskeleton allows cells to change shape and move during morphogenesis without tearing tissues apart. The Drosophila multidomain protein Canoe and its mammalian homolog afadin are crucial for this, as in their absence many events of morphogenesis fail. To define the mechanism of action for Canoe, it is being taken apart. Canoe has five folded protein domains and a long intrinsically disordered region. The largest is the Dilute domain, which is shared by Canoe and myosin V. To define the roles of this domain in Canoe, iochemical, genetic and cell biological assays were combined. AlphaFold was used to predict its structure, providing similarities and contrasts with Myosin V. Biochemical data suggested one potential shared function - the ability to dimerize. Canoe mutants were generated with the Dilute domain deleted (CnoΔDIL). Surprisingly, they were viable and fertile. CnoΔDIL localized to adherens junctions and was enriched at junctions under tension. However, when its dose was reduced, CnoΔDIL did not provide fully wild-type function. Furthermore, canoeΔDIL mutants had defects in the orchestrated cell rearrangements of eye> development. This reveals the robustness of junction-cytoskeletal connections during morphogenesis and highlights the power of natural selection to maintain protein structure. |
| Rinaldin, M., Kickuth, A., Dalton, B., Xu, Y., Di Talia, S., Brugues, J. (2024). Robust cytoplasmic partitioning by solving an intrinsic cytoskeletal instability. bioRxiv, PubMed ID: 38559072
Summary: Early development across vertebrates and insects critically relies on robustly reorganizing the cytoplasm of fertilized eggs into individualized cells. This intricate process is orchestrated by large microtubule structures that traverse the embryo, partitioning the cytoplasm into physically distinct and stable compartments. Despite the robustness of embryonic development, this study uncovered an intrinsic instability in cytoplasmic partitioning driven by the microtubule cytoskeleton. Embryos circumvent this instability through two distinct mechanisms: either by matching the cell cycle duration to the time needed for the instability to unfold or by limiting microtubule nucleation. These regulatory mechanisms give rise to two possible strategies to fill the cytoplasm, which have been experimentally demonstrated in zebrafish and Drosophila embryos, respectively. In zebrafish embryos, unstable microtubule waves fill the geometry of the entire embryo from the first division. Conversely, in Drosophila embryos, stable microtubule asters resulting from reduced microtubule nucleation gradually fill the cytoplasm throughout multiple divisions. These results indicate that the temporal control of microtubule dynamics could have driven the evolutionary emergence of species-specific mechanisms for effective cytoplasmic organization. Furthermore, this study unveils a fundamental synergy between physical instabilities and biological clocks, uncovering universal strategies for rapid, robust, and efficient spatial ordering in biological systems. | Tran, N. V., Montanari, M. P., Lubenets, D., Fischbach, L. L., Antson, H., Okada, Y., Ishimoto, Y., Tonissoo, T., Shimmi, O. (2024). α-Spectrin regulates cell shape changes during disassembly of microtubule-driven protrusions in Drosophila wings. microPublication biology, 2024 PubMed ID: 38690064
Summary: The dynamics of microtubule-mediated protrusions, termed Interplanar Amida Network (IPAN) in Drosophila pupal wing, involve cell shape changes. The molecular mechanisms underlying these processes are yet to be fully understood. This study delineates the stages of cell shape alterations during the disassembly of microtubule protrusions and underscores the pivotal role of α-Spectrin in driving these changes by regulating both the microtubule and actomyosin networks. These findings also demonstrate that α-Spectrin is required for the apical relaxation of wing epithelia during protrusion disassembly, indicating its substantial contribution to the robustness of 3D tissue morphogenesis. |
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