What's hot today:
Current papers in developmental biology and gene function
Follow @interactivefly
Tweet
|
|
What's hot today:
|
|
| ARCHIVE | Wednesday, January 31st, 2024 - Gonads |
|
What's hot today
February 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 November 2022 October 2022 September 2022 August 2022 July 2022 June 2022 May 2022 April 2022 March 2022 February 2022 January 2022 December 2021 November 2021 December 2020 July 2020 December 2019 July 2019 | Zheng, Y., Mao, B., Wang, Q., Duan, X., Chen, M. Y., Shen, W., Li, C. and Wang, Y. F. (2023). Quantitative proteomics and phosphoproteomics reveal insights into mechanisms of ocnus function in Drosophila testis development. BMC Genomics 24(1): 283. PubMed ID: 37237333
Summary: Testis has the largest number of proteins and tissue-specific proteins in animals. Knockdown of ocnus (ocn), a testis-specific gene, has been shown to result in much smaller testis with no germ cells in Drosophila. Through iTRAQ quantitative proteomics sequencing, 606 proteins were identified as having a significant and at least a 1.5-fold change in expression after ocn knockdown in fly testes; 85 were up-regulated and 521 were down-regulated. Among the differential expressed proteins (DEPs) were proteins that affected generation of precursor metabolites and energy, metabolic process, and mitochondrial transport. Protein-protein interaction (PPI) analyses of DEPs showed that several kinases and/or phosphatases interacted with Ocn. qRT-PCR confirmed 12 genes appeared in both DEGs and DEPs were significantly down-regulated after ocn knockdown in testes. Furthermore, 153 differentially expressed phosphoproteins (DEPPs), including 72 up-regulated and 94 down-regulated ones were also identified. In addition to those DEPPs associated with spermatogenesis, the other DEPPs were enriched in actin filament-based process, protein folding, and mesoderm development. Some DEPs and DEPPs were involved in Notch, JAK/STAT, and cell death pathways. The differences in protein abundance in the ocn knockdown flies might not necessarily be the direct result of differential gene regulation due to the inactivation of ocn. Nevertheless, these results suggest that the expression of ocn is essential for Drosophila testis development and that its down-regulation disturbs key signaling pathways related to cell survival and differentiation. | Tu, R., Tang, X. A., Xu, R., Ping, Z., Yu, Z. and Xie, T. (2023). Gap junction-transported cAMP from the niche controls stem cell progeny differentiation. Proc Natl Acad Sci U S A 120(35): e2304168120. PubMed ID: 37603749
Summary: The niche has been shown to control stem cell self-renewal in different tissue types and organisms. Recently, a separate niche has been proposed to control stem cell progeny differentiation, called the differentiation niche. However, it remains poorly understood whether and how the differentiation niche directly signals to stem cell progeny to control their differentiation. In the Drosophila ovary, inner germarial sheath (IGS) cells contribute to two separate niche compartments for controlling both germline stem cell (GSC) self-renewal and progeny differentiation. This study shows that IGS cells express Inx2 protein, which forms gap junctions (GJs) with germline-specific Zpg protein to control stepwise GSC lineage development, including GSC self-renewal, germline cyst formation, meiotic double-strand DNA break formation, and oocyte specification. Germline-specific Zpg and IGS-specific Inx2 knockdowns cause similar defects in stepwise GSC development. Additionally, secondary messenger cAMP is transported from IGS cells to GSCs and their progeny via GJs to activate PKA signaling for controlling stepwise GSC development. Therefore, this study demonstrates that the niche directly controls GSC progeny differentiation via the GJ-cAMP-PKA signaling axis, which provides important insights into niche control of stem cell differentiation and highlights the importance of GJ-transported cAMP in tissue regeneration. This may represent a general strategy for the niche to control adult stem cell development in various tissue types and organisms since GJs and cAMP are widely distributed. |
| Santos, I. B., Wainman, A., Garrido-Maraver, J., Pires, V., Riparbelli, M. G., Kovacs, L., Callaini, G., Glover, D. M. and Tavares A, A. (2023). Mob4 is essential for spermatogenesis in Drosophila melanogaster. Genetics 224(4). PubMed ID: 37259670
Summary: Gamete formation is essential for sexual reproduction in metazoans. Meiosis in males gives rise to spermatids that must differentiate and individualize into mature sperm. In Drosophila melanogaster, individualization of interconnected spermatids requires the formation of individualization complexes that synchronously move along the sperm bundles. This study showed that Mob4, a member of the Mps-one binder family, is essential for male fertility but has no detectable role in female fertility. Mob4 was shown to be required for proper axonemal structure and its loss leads to male sterility associated with defective spermatid individualization and absence of mature sperm in the seminal vesicles. Transmission electron micrographs of developing spermatids following mob4RNAi revealed expansion of the outer axonemal microtubules such that the 9 doublets no longer remained linked to each other and defective mitochondrial organization. Mob4 is a STRIPAK component, and male fertility is similarly impaired upon depletion of the STRIPAK components, Strip and Cka. Expression of the human Mob4 gene rescues all phenotypes of Drosophila mob4 downregulation, indicating that the gene is evolutionarily and functionally conserved. Together, this suggests that Mob4 contributes to the regulation of the microtubule- and actin-cytoskeleton during spermatogenesis through the conserved STRIPAK complex. This study advances the understanding of male infertility by uncovering the requirement for Mob4 in sperm individualization. | Ryniawec, J. M., Hannaford, M. R., Zibrat, M. E., Fagerstrom, C. J., Galletta, B. J., Aguirre, S. E., Guice, B. A., Dean, S. M., Rusan, N. M., Rogers, G. C. (2023). Cep104 is a component of the centriole distal tip complex that regulates centriole growth and contributes to Drosophila spermiogenesis. Curr Biol, 33(19):4202-4216 PubMed ID: 37729913
Summary: Proper centrosome number and function relies on the accurate assembly of centrioles, barrel-shaped structures that form the core duplicating elements of the organelle. The growth of centrioles is regulated in a cell cycle-dependent manner; while new daughter centrioles elongate during the S/G2/M phase, mature mother centrioles maintain their length throughout the cell cycle. Centriole length is controlled by the synchronized growth of the microtubules that ensheathe the centriole barrel. Although proteins exist that target the growing distal tips of centrioles, such as Cep97, these proteins are generally thought to suppress centriolar microtubule growth, suggesting that distal tips may also contain unidentified counteracting factors that facilitate microtubule polymerization. Currently, a mechanistic understanding of how distal tip proteins balance microtubule growth and shrinkage to either promote daughter centriole elongation or maintain centriole length is lacking. Using a proximity-labeling screen in Drosophila cells, this study identified Cep104 as a novel component of a group of evolutionarily conserved proteins that were collectively refered to as the distal tip complex (DTC). Cep104 was shown to regulats centriole growth and promote centriole elongation through its microtubule-binding TOG domain. Furthermore, analysis of Cep104 null flies revealed that Cep104 and Cep97 cooperate during spermiogenesis to align spermatids and coordinate individualization. Lastly, the complete DTC interactome was mapped, and Cep97 is the central scaffolding unit required to recruit DTC components to the distal tip of centrioles. |
| Yildirim, K., van Nierop, Y. S. P. and Lohmann, I. (2023). Analysis of Bub3 and Nup75 in the Drosophila male germline lineage. Cells Dev 175: 203863. PubMed ID: 37286104
Summary: Extensive communication at the stem cell-niche interface and asymmetric stem cell division is key for the homeostasis of the Drosophila male germline stem cell system. To improve understanding of these processes, the function of the mitotic checkpoint complex (MCC) component Bub3 and the nucleoporin Nup75, a component of the nuclear pore complex realizing the transport of signalling effector molecules to the nucleus, were analyzed in the Drosophila testis. By lineage-specific interference, it was found that the two genes control germline development and maintenance. Bub3 is continuously required in the germline, as its loss results in the beginning in an over-proliferation of early germ cells and later on in loss of the germline. The absence of the germline lineage in such testes has dramatic cell non-autonomous consequences, as cells co-expressing markers of hub and somatic cyst cell fates accumulate and populate in extreme cases the whole testis. This analysis of Nups showed that some of them are critical for lineage maintenance, as their depletion results in the loss of the affected lineage. In contrast, Nup75 plays a role in controlling proliferation of early germ cells but not differentiating spermatogonia and seems to be involved in keeping hub cells quiescent. In sum, this analysis shows that Bub3 and Nup75 are required for male germline development and maintenance. | Knudsen, C., Woo Seuk, K., Izumikawa, T., Nakato, E., Akiyama, T., Kinoshita-Toyoda, A., Haugstad, G., Yu, G., Toyoda, H., Nakato, H. (2023). Chondroitin sulfate is required for follicle epithelial integrity and organ shape maintenance in Drosophila. Development, 150(17) PubMed ID: 37694610
Summary: Heparan sulfate (HS) and chondroitin sulfate (CS) are evolutionarily conserved glycosaminoglycans that are found in most animal species, including the genetically tractable model organism Drosophila. In contrast to extensive in vivo studies elucidating co-receptor functions of Drosophila HS proteoglycans (PGs), only a limited number of studies have been conducted for those of CSPGs. To investigate the global function of CS in development, mutants were generated for Chondroitin sulfate synthase (Chsy), which encodes the Drosophila homolog of mammalian chondroitin synthase 1, a crucial CS biosynthetic enzyme. Characterizations of the Chsy mutants indicated that a fraction survive to adult stage, which allowed analysis of the morphology of the adult organs. In the ovary, Chsy mutants exhibited altered stiffness of the basement membrane and muscle dysfunction, leading to a gradual degradation of the gross organ structure as mutant animals aged. These observations show that normal CS function is required for the maintenance of the structural integrity of the ECM and gross organ architecture. |
Tuesday, January 30th - Adult Neural Structure and Function |
| Boyan, G., Williams, L., Ehrhardt, E. (2023). Central projections from Johnston's organ in the locust: Axogenesis and brain neuroarchitecture. Dev Genes Evol, 233(2):147-159 PubMed ID: 37695323
Summary: Johnston's organ (Jo) acts as an antennal wind-sensitive and/or auditory organ across a spectrum of insect species and its axons universally project to the brain. In the locust, this pathway is already present at mid-embryogenesis but the process of fasciculation involved in its construction has not been investigated. Terminal projections into the fine neuropilar organization of the brain also remain unresolved, information essential not only for understanding the neural circuitry mediating Jo-mediated behavior but also for providing comparative data offering insights into its evolution. In this study, neuron-specific, axon-specific, and epithelial domain labels were employed to show that the pathway to the brain of the locust is built in a stepwise manner during early embryogenesis as processes from Jo cell clusters in the pedicel fasciculate first with one another, and then with the two tracts constituting the pioneer axon scaffold of the antenna. A comparison of fasciculation patterns confirms that projections from cell clusters of Jo stereotypically associate with only one axon tract according to their location in the pedicellar epithelium, consistent with a topographic plan. At the molecular level, all neuronal elements of the Jo pathway to the brain express the lipocalin Lazarillo, a cell surface epitope that regulates axogenesis in the primary axon scaffold itself, and putatively during fasciculation of the Jo projections to the brain. Central projections from Jo first contact the primary axon scaffold of the deutocerebral brain at mid-embryogenesis, and in the adult traverse mechanosensory/motor neuropils similar to those in Drosophila. These axons then terminate among protocerebral commissures containing premotor interneurons known to regulate flight behavior. | Zhuravlev, A. V., Zalomaeva, E. S., Egozova, E. S., Sokurova, V. V., Nikitina, E. A. and Savvateeva-Popova, E. V. (2023). LIM-kinase 1 effects on memory abilities and male courtship song in Drosophila depend on the neuronal type.. Vavilovskii Zhurnal Genet Selektsii 27(3): 250-263. PubMed ID: 37293442
Summary: The signal pathway of actin remodeling, including LIM-kinase 1 (LIMK1) and its substrate cofilin, regulates multiple processes in neurons of vertebrates and invertebrates. Drosophila melanogaster is widely used as a model object for studying mechanisms of memory formation, storage, retrieval and forgetting. Previously, active forgetting in Drosophila was investigated in the standard Pavlovian olfactory conditioning paradigm. The role of specific dopaminergic neurons (DAN) and components of the actin remodeling pathway in different forms of forgetting was shown. This research investigated the role of LIMK1 in Drosophila memory and forgetting in the conditioned courtship suppression paradigm (CCSP). In the Drosophila brain, LIMK1 and p-cofilin levels appeared to be low in specific neuropil structures, including the mushroom body (MB) lobes and the central complex. At the same time, LIMK1 was observed in cell bodies, such as DAN clusters regulating memory formation in CCSP. GAL4 x UAS binary system was applied to induce limk1 RNA interference in different types of neurons. The hybrid strain with limk1 interference in MB lobes and glia showed an increase in 3-h short-term memory (STM), without significant effects on long-term memory. limk1 interference in cholinergic neurons (CHN) impaired STM, while its interference in DAN and serotoninergic neurons (SRN) also dramatically impaired the flies' learning ability. By contrast, limk1 interference in fruitless neurons (FRN) resulted in increased 15-60 min STM, indicating a possible LIMK1 role in active forgetting. Males with limk1 interference in CHN and FRN also showed the opposite trends of courtship song parameters changes. Thus, LIMK1 effects on the Drosophila male memory and courtship song appeared to depend on the neuronal type or brain structure. |
| Zhu, J., Boivin, J. C., Pang, S., Xu, C. S., Lu, Z., Saalfeld, S., Hess, H. F. and Ohyama, T. (2023). Comparative connectomics and escape behavior in larvae of closely related Drosophila species. Curr Biol 33(12): 2491-2503. PubMed ID: 37285846
Summary: Evolution has generated an enormous variety of morphological, physiological, and behavioral traits in animals. How do behaviors evolve in different directions in species equipped with similar neurons and molecular components? This study adopted a comparative approach to investigate the similarities and differences of escape behaviors in response to noxious stimuli and their underlying neural circuits between closely related drosophilid species. Drosophilids show a wide range of escape behaviors in response to noxious cues, including escape crawling, stopping, head casting, and rolling. This study found that D. santomea, compared with its close relative D. melanogaster, shows a higher probability of rolling in response to noxious stimulation. To assess whether this behavioral difference could be attributed to differences in neural circuitry, focused ion beam-scanning electron microscope volumes of the ventral nerve cord of D. santomea were generated to reconstruct the downstream partners of mdIV, a nociceptive sensory neuron in D. melanogaster. Along with partner interneurons of mdVI (including Basin-2, a multisensory integration neuron necessary for rolling) previously identified in D. melanogaster, two additional partners of mdVI were identified in D. santomea. Finally, this study showed that joint activation of one of the partners (Basin-1) and a common partner (Basin-2) in D. melanogaster increased rolling probability, suggesting that the high rolling probability in D. santomea is mediated by the additional activation of Basin-1 by mdIV. These results provide a plausible mechanistic explanation for how closely related species exhibit quantitative differences in the likelihood of expressing the same behavior. | Zhang, Y., Zhang, Y., Shen, C., Hao, S., Duan, W., Liu, L. and Wei, H. (2023). . Ionizing radiation alters functional neurotransmission in Drosophila larvae. Front Cell Neurosci 17: 1151489. PubMed ID: 37484822
Summary: Patients undergoing cranial ionizing radiation therapy for brain malignancies are at increased risk of long-term neurocognitive decline, which is poorly understood and currently untreatable. Although the molecular pathogenesis has been intensively researched in many organisms, whether and how ionizing radiation alters functional neurotransmission remains unknown. This is the first study addressing physiological changes in neurotransmission after ionizing radiation exposure. To elucidate the cellular mechanisms of radiation damage, using calcium imaging, the effects were analyzed of ionizing radiation on the neurotransmitter-evoked responses of prothoracicotropic hormone (PTTH)-releasing neurons in Drosophila larvae, which play essential roles in normal larval development. The neurotransmitters dopamine and tyramine decreased intracellular calcium levels of PTTH neurons in a dose-dependent manner. In gamma irradiated third-instar larvae, a dose of 25 Gy increased the sensitivity of PTTH neurons to dopamine and tyramine, and delayed development, possibly in response to abnormal functional neurotransmission. This irradiation level did not affect the viability and arborization of PTTH neurons and successful survival to adulthood. Exposure to a 40-Gy dose of gamma irradiation decreased the neurotransmitter sensitivity, physiological viability and axo-dendritic length of PTTH neurons. These serious damages led to substantial developmental delays and a precipitous reduction in the percentage of larvae that survived to adulthood. These results demonstrate that gamma irradiation alters neurotransmitter-evoked responses, indicating synapses are vulnerable targets of ionizing radiation. The current study provides new insights into ionizing radiation-induced disruption of physiological neurotransmitter signaling, which should be considered in preventive therapeutic interventions to reduce risks of neurological deficits after photon therapy. |
| Petsakou, A., Liu, Y., Liu, Y., Comjean, A., Hu, Y., Perrimon, N. (2023). Cholinergic neurons trigger epithelial Ca(2+) currents to heal the gut. Nature, 623(7985):122-131. PubMed ID: 37722602 ID:
Summary: A fundamental and unresolved question in regenerative biology is how tissues return to homeostasis after injury. Answering this question is essential for understanding the aetiology of chronic disorders such as inflammatory bowel diseases and cancer. This study used the Drosophila midgut to investigate this and discovered that during regeneration a subpopulation of cholinergic neurons triggers Ca(2+) currents among intestinal epithelial cells, the enterocytes, to promote return to homeostasis. It was found that downregulation of the conserved cholinergic enzyme Acetylcholine esterase in the gut epithelium enables acetylcholine from specific Eiger (TNF in mammals)-sensing cholinergic neurons to activate nicotinic receptors in innervated enterocytes. This activation triggers high Ca(2+), which spreads in the epithelium through Innexin2-Innexin7 gap junctions, promoting enterocyte maturation followed by reduction of proliferation and inflammation. Disrupting this process causes chronic injury consisting of ion imbalance, Yki (YAP in humans) activation, cell death and increase of inflammatory cytokines reminiscent of inflammatory bowel disease. Altogether, the conserved cholinergic pathway facilitates epithelial Ca(2+) currents that heal the intestinal epithelium. These findings demonstrate nerve- and bioelectric-dependent intestinal regeneration and advance current understanding of how a tissue returns to homeostasis after injury. | Long, D. R., Kinser, A., Olalde-Welling, A., Brewer, L., Lim, J., Matheny, D., Long, B., Roossien, D. H. (2023). 5-HT1A regulates axon outgrowth in a subpopulation of Drosophila serotonergic neurons. Developmental neurobiology. 83(7-8):268-281 PubMed ID: 37714743
Summary: Serotonergic neurons produce extensively branched axons that fill most of the central nervous system, where they modulate a wide variety of behaviors. Many behavioral disorders have been correlated with defective serotonergic axon morphologies. Proper behavioral output therefore depends on the precise outgrowth and targeting of serotonergic axons during development. To direct outgrowth, serotonergic neurons utilize serotonin as a signaling molecule prior to it assuming its neurotransmitter role. This process, termed serotonin autoregulation, regulates axon outgrowth, branching, and varicosity development of serotonergic neurons. However, the receptor that mediates serotonin autoregulation is unknown. This study asked if serotonin receptor 5-HT1A plays a role in serotonergic axon outgrowth and branching. Using cultured Drosophila serotonergic neurons, this study found that exogenous serotonin reduced axon length and branching only in those expressing 5-HT1A. Pharmacological activation of 5-HT1A led to reduced axon length and branching, whereas the disruption of 5-HT1A rescued outgrowth in the presence of exogenous serotonin. Altogether this suggests that 5-HT1A is a serotonin autoreceptor in a subpopulation of serotonergic neurons and initiates signaling pathways that regulate axon outgrowth and branching during Drosophila development. |
Friday, January 26th - Signaling |
| Yu, D., Dai, Q., Wang, Z., Hou, S. X. and Sun, L. V. (2023). ARF1 maintains intestinal homeostasis by modulating gut microbiota and stem cell function. Life Sci 328: 121902. PubMed ID:
Summary: The small GTPase protein ARF1 has been shown to be involved in the lipolysis pathway and to selectively kill stem cells in Drosophila melanogaster. However, the role of ARF1 in mammalian intestinal homeostasis remains elusive. This study aimed to explore the role of ARF1 in intestinal epithelial cells (IECs) and reveal the possible mechanism. IEC-specific ARF1 deletion mouse model was used to evaluate the role of ARF1 in intestine. Immunohistochemistry and immunofluorescence analyses were performed to detect specific cell type markers, and intestinal organoids were cultured to assess intestinal stem cell (ISC) proliferation and differentiation. Fluorescence in situ hybridization, 16S rRNA-seq analysis, and antibiotic treatments were conducted to elucidate the role of gut microbes in ARF1-mediated intestinal function and the underlying mechanism. Colitis was induced in control and ARF1-deficient mice by dextran sulfate sodium (DSS). RNA-seq was performed to elucidate the transcriptomic changes after ARF1 deletion. ARF1 was shown to be essential for ISC proliferation and differentiation. Loss of ARF1 increased susceptibility to DSS-induced colitis and gut microbial dysbiosis. Gut microbiota depletion by antibiotics could rescue the intestinal abnormalities to a certain extent. Furthermore, RNA-seq analysis revealed alterations in multiple metabolic pathways. This work is the first to elucidate the essential role of ARF1 in regulating gut homeostasis, and provides novel insights into the pathogenesis of intestinal diseases and potential therapeutic targets. | Zhang, J., She, M., Dai, Y., Nie, X., Tang, M. and Zeng, Q. (2023). Lmpt regulates the function of Drosophila muscle by acting as a repressor of Wnt signaling. Gene 876: 147514. PubMed ID: 37245676
Summary: LIM domain is considered to be important in mediating protein-protein interactions, and members of the LIM protein family can co-regulate tissue-specific gene expression by interacting with different transcription factors. However, its exact function in vivo remains unclear. This study demonstrates that the LIM protein family member Lmpt may act as a cofactor that interacts with other transcription factors to regulate cellular functions. This study generated Lmpt knockdown Drosophila (Lmpt-KD) using the UAS-Gal4 system. The lifespan and motility of Lmpt-KD Drosophila was assessed, and the expression of muscle-related and metabolism-related genes was analyzed using qRT-PCR. Additionally, Western blot and Top-Flash luciferase reporter assay were used to evaluate the level of the Wnt signaling pathway. This study revealed that knockdown of the Lmpt gene in Drosophila resulted in a shortened lifespan and reduced motility. A significant increase was observed in oxidative free radicals in the fly gut. Furthermore, qRT-PCR analysis indicated that knockdown of Lmpt led to decreased expression of muscle-related and metabolism-related genes in Drosophila, suggesting that Lmpt plays a crucial role in maintaining muscle and metabolic functions. Finally, it was found that reduction of Lmpt significantly upregulated the expression of Wnt signaling pathway proteins. These results demonstrate that Lmpt is essential for motility and survival in Drosophila and acts as a repressor in Wnt signaling. |
| Zhu, R., Santat, L. A., Markson, J. S., Nandagopal, N., Gregrowicz, J. and Elowitz, M. B. (2023). Reconstitution of morphogen shuttling circuits. Sci Adv 9(28): eadf9336. PubMed ID: 37436981
Summary: Developing tissues form spatial patterns by establishing concentration gradients of diffusible signaling proteins called morphogens. The bone morphogenetic protein (BMP) morphogen pathway uses a family of extracellular modulators to reshape signaling gradients by actively 'shuttling' ligands to different locations. It has remained unclear what circuits are sufficient to enable shuttling, what other patterns they can generate, and whether shuttling is evolutionarily conserved. Using a synthetic, bottom-up approach, this study compared the spatiotemporal dynamics of different extracellular circuits. Three proteins-Chordin (Drosophila Sog), Twsg (Drosophila Tsg), and the BMP-1 protease (Drosophila Tolloid)-successfully displaced gradients by shuttling ligands away from the site of production. A mathematical model explained the different spatial dynamics of this and other circuits. Last, combining mammalian and Drosophila components in the same system suggests that shuttling is a conserved capability. Together, these results reveal principles through which extracellular circuits control the spatiotemporal dynamics of morphogen signaling. | Torres, A. Y., Nano, M., Campanale, J. P., Deak, S., Montell, D. J. (2023). Activated Src kinase promotes cell cannibalism in Drosophila. J Cell Biol, 222(11) PubMed ID: >37747450
Summary: Src family kinases (SFKs) are evolutionarily conserved proteins acting downstream of receptors and regulating cellular processes including proliferation, adhesion, and migration. Elevated SFK expression and activity correlate with progression of a variety of cancers. Using the Drosophila melanogaster border cells as a model, this study reports that localized activation of a Src kinase promotes an unusual behavior: engulfment of one cell by another. By modulating Src expression and activity in the border cell cluster, it was found that increased Src kinase activity, either by mutation or loss of a negative regulator, is sufficient to drive one cell to engulf another living cell. A molecular mechanism was elucidated that requires integrins, the kinases SHARK and FAK, and Rho family GTPases, but not the engulfment receptor Draper. It is proposed that cell cannibalism is a result of aberrant phagocytosis, where cells with dysregulated Src activity fail to differentiate between living and dead or self versus non-self, thus driving this malignant behavior. |
| Tokamov, S. A., Nouri, N., Rich, A., Buiter, S., Glotzer, M., Fehon, R. G. (2023). Apical polarity and actomyosin dynamics control Kibra subcellular localization and function in Drosophila Hippo signaling. Dev Cell, 58(19): 1864-1879 PubMed ID: 37729921>
Summary: The Hippo pathway is an evolutionarily conserved regulator of tissue growth that integrates inputs from both polarity and actomyosin networks. An upstream activator of the Hippo pathway, Kibra, localizes at the junctional and medial regions of the apical cortex in epithelial cells, and medial accumulation promotes Kibra activity. This study demonstrates that cortical Kibra distribution is controlled by a tug-of-war between apical polarity and actomyosin dynamics. This study show sthat while the apical polarity network, in part via atypical protein kinase C (aPKC), tethers Kibra at the junctional cortex to silence its activity, medial actomyosin flows promote Kibra-mediated Hippo complex formation at the medial cortex, thereby activating the Hippo pathway. This study provides a mechanistic understanding of the relationship between the Hippo pathway, polarity, and actomyosin cytoskeleton, and it offers novel insights into how fundamental features of epithelial tissue architecture can serve as inputs into signaling cascades that control tissue growth, patterning, and morphogenesis. | Zhou, Y., Guan, J., Meng, G., Fan, W., Ge, C., Niu, C., Cheng, Y., Fu, Y., Lu, Y. and Wei, Y. (2023). The RagA GTPase protects young egg chambers in Drosophila. Cell Rep 42(6): 112631. PubMed ID: 37302067
Summary: The preservation of female fertility under unfavorable conditions is essential for animal reproduction. Inhibition of the target of rapamycin complex 1 (TORC1) is indispensable for Drosophila young egg chamber maintenance under nutrient starvation. This study shows that knockdown of RagA results in young egg chamber death independent of TORC1 hyperactivity. RagA RNAi ovaries have autolysosomal acidification and degradation defects, which make the young egg chambers sensitive to autophagosome augmentation. Meanwhile, RagA RNAi ovaries have nuclear-localized Mitf, which promotes autophagic degradation and protects young egg chambers under stress. Interestingly, GDP-bound RagA rescues autolysosome defects, while GTP-bound RagA rescues Mitf nuclear localization in RagA RNAi young egg chambers. Moreover, Rag GTPase activity, rather than TORC1 activity, controls Mitf cellular localization in the Drosophila germ line. This work suggests that RagA separately controls autolysosomal acidification and Mitf activity in the Drosophila young egg chambers. |
Thursday, January 25th - Evolution |
| Zivanovic, G., Arenas, C. and Mestres, F. (2023). The Adaptive Value of Chromosomal Inversions and Climatic Change-Studies on the Natural Populations of Drosophila subobscura from the Balkans. Insects 14(7). PubMed ID: 37504602
Summary: The adaptive value of the Drosophila subobscura chromosomal inversion polymorphism with regard to environmental effects is well-known. However, the specific details of the inversion adaptations to the global warming scenario deserve to be analyzed. Toward this aim, polymorphism and karyotypes were studied in 574 individuals from Petnica (Serbia) in annual samples taken in June for the period 2019-2022. Comparing the results of Petnica (Cfa: humid subtropical climate) with those from Avala (Serbia: Cfb, temperate oceanic climate) and Font Groga (Barcelona, Spain; Csa: hot-summer Mediterranean climate), significant differences were observed for their chromosomal polymorphism. In Petnica, inversions from U and E chromosomes mainly reacted significantly with regard to temperature, humidity, and rainfall. Moreover, the inversion polymorphism from Petnica (2019-2022) was compared with that from 1995. In this period, a significant increase in mean and maximum temperature was observed. However, to properly explain the observed variations of inversions over time, it was necessary to carefully analyze annual seasonal changes and particular heat wave episodes. Interestingly, yearly fluctuations of U chromosome 'warm'-adapted inversions corresponded with opposite changes in 'non-thermal' inversions. Perhaps these types of inversions were not correctly defined with regard to thermal adaptation, or these fluctuations were also due to adaptations to other physical and/or biological variables. Finally, a joint study of chromosomal inversion polymorphism from many Balkan populations of D. subobscura indicated that different climatic regions presented distinct composition, including thermal-adapted inversions. | Vedanayagam, J., Herbette, M., Mudgett, H., Lin, C. J., Lai, C. M., McDonough-Goldstein, C., Dorus, S., Loppin, B., Meiklejohn, C., Dubruille, R. and Lai, E. C. (2023). Essential and recurrent roles for hairpin RNAs in silencing de novo sex chromosome conflict in Drosophila simulans. PLoS Biol 21(6): e3002136. PubMed ID: 37289846
Summary: Meiotic drive loci distort the normally equal segregation of alleles, which benefits their own transmission even in the face of severe fitness costs to their host organism. However, relatively little is known about the molecular identity of meiotic drivers, their strategies of action, and mechanisms that can suppress their activity. This study presents data from the fruitfly Drosophila simulans that address these questions. A family of de novo, protamine-derived X-linked selfish genes (the Dox gene family: Distorter on the X-which is found on the X chromosome and kills Y chromosome-bearing sperm) was demonstrated to be silenced by a pair of newly emerged hairpin RNA (hpRNA) small interfering RNA (siRNA)-class loci, Nmy and Tmy. In the w[XD1] genetic background, knockout of nmy derepresses Dox and MDox in testes and depletes male progeny, whereas knockout of tmy causes misexpression of PDox genes and renders males sterile. Importantly, genetic interactions between nmy and tmy mutant alleles reveal that Tmy also specifically maintains male progeny for normal sex ratio. The Dox loci are functionally polymorphic within D. simulans, such that both nmy-associated sex ratio bias and tmy-associated sterility can be rescued by wild-type X chromosomes bearing natural deletions in different Dox family genes. Finally, using tagged transgenes of Dox and PDox2, the first experimental evidence is provided that Dox family genes encode proteins that are strongly derepressed in cognate hpRNA mutants. Altogether, these studies support a model in which protamine-derived drivers and hpRNA suppressors drive repeated cycles of sex chromosome conflict and resolution that shape genome evolution and the genetic control of male gametogenesis. |
| Kannan, A., Dugand, R. J., Appleton, N. C., Chenoweth, S. F., Sgro, C. M., McGuigan, K. (2023). Environmental dependence of mutational (co)variances of adaptive traits. Evolution, 77(11):2341-2351. PubMed ID: 37668059
Summary: Standing genetic variation, and capacity to adapt to environment change, will ultimately depend on the fitness effects of mutations across the range of environments experienced by contemporary, panmictic, populations. This study investigated how mild perturbations in diet and temperature affect mutational (co)variances of traits that evolve under climatic adaptation, and contribute to individual fitness in Drosophila serrata. Egg-to-adult viability, development time and wing size were assessed of 64 lines that had diverged from one another via spontaneous mutation over 30 generations of brother-sister mating. The results suggested most mutations have directionally concordant (i.e., synergistic) effects in all environments and both sexes. However, elevated mutational variance under reduced macronutrient conditions suggested environment-dependent variation in mutational effect sizes for development time. Evidence was also observed for antagonistic effects under standard versus reduced macronutrient conditions, where these effects were further contingent on temperature (for development time) or sex (for size). Diet also influenced the magnitude and sign of mutational correlations between traits, although this result was largely due to a single genotype (line), which may reflect a rare, large effect mutation. Overall, these results suggest environmental heterogeneity and environment-dependency of mutational effects could contribute to the maintenance of genetic variance. | Vedanayagam, J., Lin, C. J., Papareddy, R., Nodine, M., Flynt, A. S., Wen, J. and Lai, E. C. (2023). Regulatory logic of endogenous RNAi in silencing de novo genomic conflicts. PLoS Genet 19(6): e1010787. PubMed ID: 37343034
Summary: Although the biological utilities of endogenous RNAi (endo-RNAi) have been largely elusive, recent studies reveal its critical role in the non-model fruitfly Drosophila simulans to suppress selfish genes, whose unchecked activities can severely impair spermatogenesis. In particular, hairpin RNA (hpRNA) loci generate endo-siRNAs that suppress evolutionary novel, X-linked, meiotic drive loci. The consequences of deleting even a single hpRNA (Nmy) in males are profound, as such individuals are nearly incapable of siring male progeny. In this study, comparative genomic analyses of D. simulans and D. melanogaster mutants of the core RNAi factor dcr-2 reveal a substantially expanded network of recently-emerged hpRNA-target interactions in the former species. The de novo hpRNA regulatory network in D. simulans provides insight into molecular strategies that underlie hpRNA emergence and their potential roles in sex chromosome conflict. In particular, these data support the existence of ongoing rapid evolution of Nmy/Dox-related networks, and recurrent targeting of testis HMG-box loci by hpRNAs. Importantly, the impact of the endo-RNAi network on gene expression flips the convention for regulatory networks, since strong derepression of targets of the youngest hpRNAs was observed, but only mild effects on the targets of the oldest hpRNAs. These data suggest that endo-RNAi are especially critical during incipient stages of intrinsic sex chromosome conflicts, and that continual cycles of distortion and resolution may contribute to speciation. |
| Yıldırım, B. and Vogl, C. (2023). Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract. J Evol Biol. PubMed ID: 37564008
Summary: Among eukaryotes, the major spliceosomal pathway is highly conserved. While long introns may contain additional regulatory sequences, the ones in short introns seem to be nearly exclusively related to splicing. Although these regulatory sequences involved in splicing are well-characterized, little is known about their evolution. At the 3' end of introns, the splice signal nearly universally contains the dimer AG, which consists of purines, and the polypyrimidine tract upstream of this 3' splice signal is characterized by over-representation of pyrimidines. If the over-representation of pyrimidines in the polypyrimidine tract is also due to avoidance of a premature splicing signal, it is hypothesize that AG should be the most under-represented dimer. Through the use of DNA-strand asymmetry patterns, this prediction was confirmed in fruit flies of the genus Drosophila and by comparing the asymmetry patterns to a presumably neutrally evolving region, the selection strength acting on each motif was quantified. Moreover, the inference and simulation method of this study revealed that the best explanation for the base composition evolution of the polypyrimidine tract is the joint action of purifying selection against a spurious 3' splice signal and the selection for pyrimidines. Patterns of asymmetry in other eukaryotes indicate that avoidance of premature splicing similarly affects the nucleotide composition in their polypyrimidine tracts. | Chen, J., Gish, C. M., Fransen, J. W., Salazar-Gatzimas, E., Clark, D. A., Borghuis, B. G. (2023). Direct comparison reveals algorithmic similarities in fly and mouse visual motion detection. iScience, 26(10):107928 PubMed ID: 37810236
Summary: Evolution has equipped vertebrates and invertebrates with neural circuits that selectively encode visual motion. While similarities in the computations performed by these circuits in mouse and fruit fly have been noted, direct experimental comparisons have been lacking. Because molecular mechanisms and neuronal morphology in the two species are distinct, this study directly compared motion encoding in these two species at the algorithmic level, using matched stimuli and focusing on a pair of analogous neurons, the mouse ON starburst amacrine cell (ON SAC) and Drosophila T4 neurons. It was found that the cells share similar spatiotemporal receptive field structures, sensitivity to spatiotemporal correlations, and tuning to sinusoidal drifting gratings, but differ in their responses to apparent motion stimuli. Both neuron types showed a response to summed sinusoids that deviates from models for motion processing in these cells, underscoring the similarities in their processing and identifying response features that remain to be explained. |
Monday, January 22nd - Enhancers and Transcriptional Regulation |
| Thompson, K. D., Suber, W., Nicholas, R., Arnosti, D. N. (2023). Long-range repression by ecdysone receptor on complex enhancers of the insulin receptor gene. Fly (Austin), 17(1):2242238. PubMed ID: 37621079
Summary: The insulin signalling pathway is evolutionarily conserved throughout metazoans, playing key roles in development, growth, and metabolism. Misregulation of this pathway is associated with a multitude of disease states including diabetes, cancer, and neurodegeneration. The human insulin receptor gene (INSR) is widely expressed throughout development and was previously described as a 'housekeeping' gene. Yet, there is abundant evidence that this gene is expressed in a cell-type specific manner, with dynamic regulation in response to environmental signals. The Drosophila insulin-like receptor gene (InR) is homologous to the human INSR gene and was previously shown to be regulated by multiple transcriptional elements located primarily within the introns of the gene. These elements were roughly defined in ~1.5 kbp segments, but an understanding of the potential detailed mechanisms of their regulation is lacking. The substructure of these cis-regulatory elements was characterized in Drosophila S2 cells, focusing on regulation through the ecdysone receptor (EcR) and the dFOXO transcription factor. By identifying specific locations of activators and repressors within 300 bp subelements, this study showed that some previously identified enhancers consist of relatively compact clusters of activators, while others have a distributed architecture not amenable to further reduction. In addition, these assays uncovered a long-range repressive action of unliganded EcR. The complex transcriptional circuitry likely endows InR with a highly flexible and tissue-specific response to tune insulin signalling. Further studies will provide insights to demonstrate the impact of natural variation in this gene's regulation, applicable to human genetic studies. | Nowling, R. J., Njoya, K., Peters, J. G., Riehle, M. M. (2023). Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique. Frontiers in cellular and infection microbiology, 13:1182567 PubMed ID: >37600946
Summary: Various sequencing based approaches are used to identify and characterize the activities of cis-regulatory elements in a genome-wide fashion. The activities of cis-regulatory elements such as enhancers, promoters, and repressors are determined by their sequence and secondary processes such as chromatin accessibility, DNA methylation, and bound histone markers. This study used machine learning models to evaluate the accuracy with which cis-regulatory elements identified by various commonly used sequencing techniques can be predicted by their underlying sequence alone to distinguish between cis-regulatory activity that is reflective of sequence content versus secondary processes. Models trained and evaluated on D. melanogaster sequences identified through DNase-seq and STARR-seq are significantly more accurate than models trained on sequences identified by H3K4me1, H3K4me3, and H3K27ac ChIP-seq, FAIRE-seq, and ATAC-seq. These results suggest that the activity detected by DNase-seq and STARR-seq can be largely explained by underlying DNA sequence, independent of secondary processes. Experimentally, a subset of DNase-seq and H3K4me1 ChIP-seq sequences were tested for enhancer activity using luciferase assays and compared with previous tests performed on STARR-seq sequences. The experimental data indicated that STARR-seq sequences are substantially enriched for enhancer-specific activity, while the DNase-seq and H3K4me1 ChIP-seq sequences are not. Taken together, these results indicate that the DNase-seq approach identifies a broad class of regulatory elements of which enhancers are a subset and the associated data are appropriate for training models for detecting regulatory activity from sequence alone, STARR-seq data are best for training enhancer-specific sequence models, and H3K4me1 ChIP-seq data are not well suited for training and evaluating sequence-based models for cis-regulatory element prediction. |
| Sloutskin, A., Itzhak, D., Vogler, G., Ideses, D., Alter, H., Shachar, H., Doniger, T., Frasch, M., Bodmer, R., Duttke, S. H. and Juven-Gershon, T. (2023). A single DPE core promoter motif contributes to in vivo transcriptional regulation and affects cardiac function. bioRxiv. PubMed ID: 37398300
Summary: Transcription is initiated at the core promoter, which confers specific functions depending on the unique combination of core promoter elements. The downstream core promoter element (DPE) is found in many genes related to heart and mesodermal development. However, the function of these core promoter elements has thus far been studied primarily in isolated, in vitro or reporter gene settings. tinman (tin) encodes a key transcription factor that regulates the formation of the dorsal musculature and heart. Pioneering a novel approach utilizing both CRISPR and nascent transcriptomics, this study showed that a substitution mutation of the functional tin DPE motif within the natural context of the core promoter results in a massive perturbation of Tinman's regulatory network orchestrating dorsal musculature and heart formation. Mutation of endogenous tin DPE reduced the expression of tin and distinct target genes, resulting in significantly reduced viability and an overall decrease in adult heart function. This study has demonstrated the feasibility and importance of characterizing DNA sequence elements in vivo in their natural context, and accentuate the critical impact a single DPE motif has during Drosophila embryogenesis and functional heart formation. | van den Berg, L., Kokki, K., Wowro, S. J., Petricek, K. M., Deniz, O., Stegmann, C. A., Robciuc, M., Teesalu, M., Melvin, R. G., Nieminen, A. I., Schupp, M. and Hietakangas, V. (2023). Sugar-responsive inhibition of Myc-dependent ribosome biogenesis by Clockwork orange. Cell Rep 42(7): 112739. PubMed ID: 37405919
Summary: The ability to feed on a sugar-containing diet depends on a gene regulatory network controlled by the intracellular sugar sensor Mondo/ChREBP-Mlx, which remains insufficiently characterized. This study presents a genome-wide temporal clustering of sugar-responsive gene expression in Drosophila larvae. Gene expression programs responding to sugar feeding were identified, including downregulation of ribosome biogenesis genes, known targets of Myc. Clockwork orange (CWO), a component of the circadian clock, is found to be a mediator of this repressive response and to be necessary for survival on a high-sugar diet. CWO expression is directly activated by Mondo-Mlx, and it counteracts Myc through repression of its gene expression and through binding to overlapping genomic regions. CWO mouse ortholog BHLHE41 has a conserved role in repressing ribosome biogenesis genes in primary hepatocytes. Collectively, these data uncover a cross-talk between conserved gene regulatory circuits balancing the activities of anabolic pathways to maintain homeostasis during sugar feeding. |
| Zhao, J., Perkins, M. L., Norstad, M. and Garcia, H. G. (2023). A bistable autoregulatory module in the developing embryo commits cells to binary expression fates. Curr Biol 33(14): 2851-2864 PubMed ID: 37453424
Summary: Bistable autoactivation has been proposed as a mechanism for cells to adopt binary fates during embryonic development. However, it is unclear whether the autoactivating modules found within developmental gene regulatory networks are bistable, unless their parameters are quantitatively determined. This study combined in vivo live imaging with mathematical modeling to dissect the binary cell fate dynamics of the fruit fly pair-rule gene fushi tarazu (ftz), which is regulated by two known enhancers: the early (non-autoregulating) element and the autoregulatory element. Live imaging of transcription and protein concentration in the blastoderm revealed that binary Ftz fates are achieved as Ftz expression rapidly transitions from being dictated by the early element to the autoregulatory element. Moreover, this study discovered that Ftz concentration alone is insufficient to activate the autoregulatory element, and that this element only becomes responsive to Ftz at a prescribed developmental time. Based on these observations,a dynamical systems model was developed, and its kinetic parameters were quantitated directly from experimental measurements. This model demonstrated that the ftz autoregulatory module is indeed bistable and that the early element transiently establishes the content of the binary cell fate decision to which the autoregulatory module then commits. Further in silico analysis revealed that the autoregulatory element locks the Ftz fate quickly, within 35 min of exposure to the transient signal of the early element. Overall, this work confirms the widely held hypothesis that autoregulation can establish developmental fates through bistability and, most importantly, provides a framework for the quantitative dissection of cellular decision-making. | Moudgil, A., Sobti, R. C., Kaur, T. (2023). In-silico identification and comparison of transcription factor binding sites cluster in anterior-posterior patterning genes in Drosophila melanogaster and Tribolium castaneum. PLoS One, 18(8):e0290035 PubMed ID: 37590227
Summary: The cis-regulatory data that help in transcriptional regulation is arranged into modular pieces of a few hundred base pairs called CRMs (cis-regulatory modules) and numerous binding sites for multiple transcription factors are prominent characteristics of these cis-regulatory modules. The present study was designed to localize transcription factor binding site (TFBS) clusters on twelve Anterior-posterior (A-P) genes in Tribolium castaneum and compare them to their orthologous gene enhancers in Drosophila melanogaster. Out of the twelve A-P patterning genes, six were gap genes (Kruppel, Knirps, Tailless, Hunchback, Giant, and Caudal) and six were pair rule genes (Hairy, Runt, Even-skipped, Fushi-tarazu, Paired, and Odd-skipped). The genes along with 20 kb upstream and downstream regions were scanned for TFBS clusters using the Motif Cluster Alignment Search Tool (MCAST), a bioinformatics tool that looks for set of nucleotide sequences for statistically significant clusters of non-overlapping occurrence of a given set of motifs. The motifs used in the current study were Hunchback, Caudal, Giant, Kruppel, Knirps, and Even-skipped. The results of the MCAST analysis revealed the maximum number of TFBS for Hunchback, Knirps, Caudal, and Kruppel in both D. melanogaster and T. castaneum, while Bicoid TFBS clusters were found only in D. melanogaster. The size of all the predicted TFBS clusters was less than 1kb in both insect species. These sequences revealed more transversional sites (Tv) than transitional sites (Ti) and the average Ti/Tv ratio was 0.75. |
Friday, January 19th - Disease Models |
| Yue, W., Deng, X., Wang, Z., Jiang, M., Hu, R., Duan, Y., Wang, Q., Cui, J. and Fang, Y. (2023). Inhibition of the MEK/ERK pathway suppresses immune overactivation and mitigates TDP-43 toxicity in a Drosophila model of ALS. Immun Ageing 20(1): 27. PubMed ID: 37340309
Summary: TDP-43 is an important DNA/RNA-binding protein that is associated with age-related neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD); however, its pathomechanism is not fully understood. In a transgenic RNAi screen using Drosophila as a model, this study uncovered that knockdown (KD) of Dsor1 (the Drosophila MAPK kinase dMEK) suppressed TDP-43 toxicity without altering TDP-43 phosphorylation or protein levels. Further investigation revealed that the Dsor1 downstream gene rl (dERK) was abnormally upregulated in TDP-43 flies, and neuronal overexpression of dERK induced profound upregulation of antimicrobial peptides (AMPs). A robust immune overactivation was pbserved in TDP-43 flies, which could be suppressed by downregulation of the MEK/ERK pathway in TDP-43 fly neurons. Furthermore, neuronal KD of abnormally increased AMPs improved the motor function of TDP-43 flies. On the other hand, neuronal KD of Dnr1, a negative regulator of the Drosophila immune deficiency (IMD) pathway, activated the innate immunity and boosted AMP expression independent of the regulation by the MEK/ERK pathway, which diminished the mitigating effect of RNAi-dMEK on TDP-43 toxicity. Finally, this study showed that an FDA-approved MEK inhibitor trametinib markedly suppressed immune overactivation, alleviated motor deficits and prolonged the lifespan of TDP-43 flies, but did not exhibit a lifespan-extending effect in Alzheimer disease (AD) or spinocerebellar ataxia type 3 (SCA3) fly models. Together, these findings suggest an important role of abnormal elevation of the MEK/ERK signaling and innate immunity in TDP-43 pathogenesis and propose trametinib as a potential therapeutic agent for ALS and other TDP-43-related diseases. | Yamada, M., Nitta, Y., Uehara, T., Suzuki, H., Miya, F., Takenouchi, T., Tamura, M., Ayabe, S., Yoshiki, A., Maeno, A., Saga, Y., Furuse, T., Yamada, I., Okamoto, N., Kosaki, K. and Sugie, A. (2023). Heterozygous loss-of-function DHX9 variants are associated with neurodevelopmental disorders: Human genetic and experimental evidences. Eur J Med Genet 66(8): 104804. PubMed ID: 37369308
Summary: DExH-box helicases are involved in unwinding of RNA and DNA. Among the 16 DExH-box genes, monoallelic variants of DHX16, DHX30, DHX34, and DHX37 are known to be associated with neurodevelopmental disorders. In particular, DHX30 is well established as a causative gene for neurodevelopmental disorders. Germline variants of DHX9, the closest homolog of DHX30, have not been reported until now as being associated with congenital disorders in humans, except that one de novo heterozygous variant, p.(Arg1052Gln) of the gene was identified during comprehensive screening in a patient with autism; unfortunately, the phenotypic details of this individual are unknown. This study reports a patient with a heterozygous de novo missense variant, p.(Gly414Arg) of DHX9 who presented with a short stature, intellectual disability, and ventricular non-compaction cardiomyopathy. The variant was located in the glycine codon of the ATP-binding site, G-C-G-K-T. To assess the pathogenicity of these variants, transgenic Drosophila lines were generated expressing human wild-type and mutant DHX9 proteins (Drosophila homolog: maleless): 1) the mutant proteins showed aberrant localization both in the nucleus and the cytoplasm; 2) ectopic expression of wild-type protein in the visual system led to the rough eye phenotype, whereas expression of the mutant proteins had minimal effect; 3) overexpression of the wild-type protein in the retina led to a reduction in axonal numbers, whereas expression of the mutant proteins had a less pronounced effect. Furthermore, in a gene-editing experiment of Dhx9 G416 to R416, corresponding to p.(Gly414Arg) in humans, heterozygous mice showed a reduced body size, reduced emotionality, and cardiac conduction abnormality. In conclusion, this study has established that heterozygosity for a loss-of-function variant of DHX9 can lead to a new neurodevelopmental disorder. |
| Yu, M., Ye, H., De-Paula, R. B., Mangleburg, C. G., Wu, T., Lee, T. V., Li, Y., Duong, D., Phillips, B., Cruchaga, C., Allen, G. I., Seyfried, N. T., Al-Ramahi, I., Botas, J. and Shulman, J. M. (2023). Functional screening of lysosomal storage disorder genes identifies modifiers of alpha-synuclein neurotoxicity. PLoS Genet 19(5): e1010760. PubMed ID: 37200393
Summary: Heterozygous variants in the glucocerebrosidase (GBA; see Drosophila Gba1a) gene are common and potent risk factors for Parkinson's disease (PD). GBA also causes the autosomal recessive lysosomal storage disorder (LSD), Gaucher disease, and emerging evidence from human genetics implicates many other LSD genes in PD susceptibility. This study has systemically tested 86 conserved fly homologs of 37 human LSD genes for requirements in the aging adult Drosophila brain and for potential genetic interactions with neurodegeneration caused by α-synuclein (αSyn), which forms Lewy body pathology in PD. The screen identifies 15 genetic enhancers of αSyn-induced progressive locomotor dysfunction, including knockdown of fly homologs of GBA and other LSD genes with independent support as PD susceptibility factors from human genetics (SCARB2, SMPD1, CTSD, GNPTAB, SLC17A5). For several genes, results from multiple alleles suggest dose-sensitivity and context-dependent pleiotropy in the presence or absence of αSyn. Homologs of two genes causing cholesterol storage disorders, Npc1a / NPC1 and Lip4 / LIPA, were independently confirmed as loss-of-function enhancers of αSyn-induced retinal degeneration. The enzymes encoded by several modifier genes are upregulated in αSyn transgenic flies, based on unbiased proteomics, revealing a possible, albeit ineffective, compensatory response. Overall, these results reinforce the important role of lysosomal genes in brain health and PD pathogenesis, and implicate several metabolic pathways, including cholesterol homeostasis, in αSyn-mediated neurotoxicity. | Zhou, H., Wang, J. and Wen, T. (2023). The molecular neural mechanism underlying the acceleration of brain aging due to Dcf1 deficiency. Mol Cell Neurosci 126: 103884. PubMed ID: 37506857
Summary: Owing to the continuous increase in human life expectancy, the management of aging-related diseases has become an urgent issue. The brain dominates the central nervous system; therefore, brain aging is a key area of aging-related research. Previous work uncovered that dendritic cell factor 1 (Dcf1) maintains the stemness of neural stem cells and its expression in Drosophila can prolong lifespan, suggesting an association between Dcf1 and aging; however, the specific underlying neural mechanism remains unclear. The present study showed for the first time that hippocampal neurogenesis is decreased in aged Dcf1(-/-) mice, which leads to a decrease in the number of brain neurons and an increased number of senescent cells. Moreover, astrocytes proliferate abnormally and express elevated mRNA levels of aging-related factors, in addition to displaying increased activation of Akt and Foxo3a. Finally, behavioral tests confirm that aged Dcf1(-/-) mice exhibit a significant decline in cognitive abilities related to learning and memory. In conclusion, this study revealed a novel mechanism underlying brain aging triggered by Dcf1 deficiency at the molecular, cellular, tissue, and behavioral levels, providing a new perspective for the exploration of brain aging. |
| Xu, W., Rustenhoven, J., Nelson, C. A., Dykstra, T., Ferreiro, A., Papadopoulos, Z., Burnham, C. D., Dantas, G., Fremont, D. H. and Kipnis, J. (2023). A novel immune modulator IM33 mediates a glia-gut-neuronal axis that controls lifespan. Neuron. PubMed ID: 37582366
Summary: Aging is a complex process involving various systems and behavioral changes. Altered immune regulation, dysbiosis, oxidative stress, and sleep decline are common features of aging, but their interconnection is poorly understood. Using Drosophila, this study discovered that IM33, a novel immune modulator, and its mammalian homolog, secretory leukocyte protease inhibitor (SLPI), are upregulated in old flies and old mice, respectively. Knockdown of IM33 in glia elevates the gut reactive oxygen species (ROS) level and alters gut microbiota composition, including increased Lactiplantibacillus plantarum abundance, leading to a shortened lifespan. Additionally, dysbiosis induces sleep fragmentation through the activation of insulin-producing cells in the brain, which is mediated by the binding of Lactiplantibacillus plantarum-produced DAP-type peptidoglycan to the peptidoglycan recognition protein LE (PGRP-LE) receptor. Therefore, IM33 plays a role in the glia-microbiota-neuronal axis, connecting neuroinflammation, dysbiosis, and sleep decline during aging. Identifying molecular mediators of these processes could lead to the development of innovative strategies for extending lifespan. | Zhang, F., Wang, L., Jin, J., Pang, Y., Shi, H., Fang, Z., Wang, H., Du, Y., Hu, Y., Zhang, Y., Ding, X. and Zhu, Z. (2023). Insights into the genetic influences of the microbiota on the life span of a host. Front Microbiol 14: 1138979. PubMed ID: 37601381
Summary: Escherichia coli (E. coli) mutant strains have been reported to extend the life span of Caenorhabditis elegans (C. elegans). However, the specific mechanisms through which the genes and pathways affect aging are not yet clear. In this study, Drosophila melanogaster (fruit fly) was fed various E. coli single-gene knockout strains to screen mutant strains with an extended lifespan. The results showed that D. melanogaster fed with E. coli purE had the longest mean lifespan, which was verified by C. elegans. RNA-sequencing and analysis was conducted of C. elegans fed with E. coli purE (a single-gene knockout mutant) to further explore the underlying molecular mechanism. Differential gene expression (DGE) analysis, enrichment analysis, and gene set enrichment analysis (GSEA) to screen vital genes and modules with significant changes in overall expression. These results suggest that E. coli mutant strains may affect the host lifespan by regulating the protein synthesis rate (cfz-2) and ATP level (catp-4). To conclude, this study could provide new insights into the genetic influences of the microbiota on the life span of a host and a basis for developing anti-aging probiotics and drugs. |
Wednesday, January 17th - Enzymes and Protein Expression, Evolution, Structure and Function |
| Weingartner, K. A., Tran, T., Tripp, K. W. and Kavran, J. M. (2023). Dimerization and autophosphorylation of the MST family of kinases are controlled by the same set of residues. Biochem J 480(15): 1165-1182. PubMed ID: 37459121
Summary: The Hippo pathway controls tissue growth and regulates stem cell fate through the activities of core kinase cassette that begins with the Sterile 20-like kinase MST1/2. Activation of MST1/2 relies on trans-autophosphorylation but the details of the mechanisms regulating that reaction are not fully elucidated. Proposals include dimerization as a first step and include multiple models for potential kinase-domain dimers. Efforts to verify and link these dimers to trans-autophosphorylation were unsuccessful. The link between dimerization and trans-autophosphorylation for MST2 and the entire family of MST kinases was explored. Crystal lattice contacts of structures of MST kinases was examined, and an ensemble of kinase-domain dimers compatible with trans-autophosphorylation was identified. These dimers share a common dimerization interface comprised of the activation loop and αG-helix while the arrangements of the kinase-domains within the dimer varied depending on their activation state. The dimerization interface was identfied, and its function was determined using MST2. Variants bearing alanine substitutions of the αG-helix prevented dimerization of the MST2 kinase domain both in solution and in cells. These substitutions also blocked autophosphorylation of full-length MST2 and its Drosophila homolog Hippo in cells. These variants retain the same secondary structure as wild-type and capacity to phosphorylate a protein substrate, indicating the loss of MST2 activation can be directly attributed to a loss of dimerization rather than loss of either fold or catalytic function. Together this data functionally links dimerization and autophosphorylation for MST2 and suggests this activation mechanism is conserved across both species and the entire MST family. | Zhang, Y., Huang, Q., Sheng, C., Liu, G., Zhang, K., Jia, Z., Tang, T., Mao, X., Jones, A. K., Han, Z. and Zhao, C. (2023). G3'MTMD3 in the insect GABA receptor subunit, RDL, confers resistance to broflanilide and fluralaner. PLoS Genet 19(6): e1010814. PubMed ID: 37384781
Summary: Meta-diamides (e.g. broflanilide) and isoxazolines (e.g. fluralaner) are novel insecticides that target the resistant to dieldrin (RDL) subunit of insect γ-aminobutyric acid receptors (GABARs). This study used in silico analysis to identify residues that are critical for the interaction between RDL and these insecticides. Substitution of glycine at the third position (G3') in the third transmembrane domain (TMD3) with methionine (G3'M TMD3), which is present in vertebrate GABARs, had the strongest effect on fluralaner binding. This was confirmed by expression of RDL from the rice stem borer, Chilo suppressalis (CsRDL) in oocytes of the African clawed frog, Xenopus laevis, where the G3'MTMD3 mutation almost abolished the antagonistic action of fluralaner. Subsequently, G3'MTMD3 was introduced into the Rdl gene of the fruit fly, Drosophila melanogaster, using the CRISPR/Cas9 system. Larvae of heterozygous lines bearing G3'MTMD3 did not show significant resistance to avermectin, fipronil, broflanilide, and fluralaner. However, larvae homozygous for G3'MTMD3 were highly resistant to broflanilide and fluralaner whilst still being sensitive to fipronil and avermectin. Also, homozygous lines showed severely impaired locomotivity and did not survive to the pupal stage, indicating a significant fitness cost associated with G3'MTMD3. Moreover, the M3'GTMD3 mutation in the mouse Mus musculus α1β2 GABAR increased sensitivity to fluralaner. Taken together, these results provide convincing in vitro and in vivo evidence for both broflanilide and fluralaner acting on the same amino acid site, as well as insights into potential mechanisms leading to target-site resistance to these insecticides. In addition, these findings could guide further modification of isoxazolines to achieve higher selectivity for the control of insect pests with minimal effects on mammals. |
| Tomihara, K. and Kiuchi, T. (2023). Disruption of a BTB-ZF transcription factor causes female sterility and melanization in the larval body of the silkworm, Bombyx mori. Insect Biochem Mol Biol 159: 103982. PubMed ID: 37356736
Summary: The dilute black (bd) of the silkworm Bombyx mori is a recessive mutant that produces a grayish-black color in the larval integument, instead of the characteristic white color found in wild-type larvae. In addition, eggs produced by bd females are sterile due to a deficiency in the micropylar apparatus. This study identified candidate genes responsible for the bd phenotype using publicly available RNA-seq data. One of these candidate genes was homologous to the maternal gene required for meiosis (mamo) of Drosophila melanogaster, which encodes a broad-complex, tramtrack, and bric-à-brac-zinc finger (BTB-ZF) transcription factor essential for female fertility. In three independent bd strains, the expression of the B. mori mamo (Bmmamo) was downregulated in the larval integument. Using a CRISPR/Cas9-mediated knockout strategy, it was found that Bmmamo knockout mutants exhibit a grayish-black color in the larval integument and female infertility. Moreover, larvae obtained from the complementation cross between bd/+ mutants and heterozygous knockouts for the Bmmamo also exhibited a grayish-black color, indicating that Bmmamo is responsible for the bd phenotype. Gene expression analysis using Bmmamo knockout mutants suggested that the BmMamo protein suppresses the expression of melanin synthesis genes. Previous comparative genome analysis revealed that the Bmmamo was selected during silkworm domestication, and this study found that Bmmamo expression in the larval integument is higher in B. mori than in the wild silkworm B. mandarina, suggesting that the Bmmamo is involved in domestication-associated pigmentation changes of the silkworm. | Zhao, J., Lin, L., Hadiatullah, H., Chen, W., Huang, J., Wu, S., Murayama, T. and Yuchi, Z. (2023). Characterization of Six Diamide Insecticides on Ryanodine Receptor: Resistance and Species Selectivity. J Agric Food Chem 71(29): 11001-11007. PubMed ID: 37462137
Summary: Ryanodine receptor (RyR) has been used as an insecticide target to control many destructive agricultural pests. The effectiveness of these insecticides has been limited by the spread of resistance mutations identified in pest RyRs, but the detailed molecular impacts of the individual mutations on the activity of different diamide compounds have not been fully explored. This study created five HEK293 cell lines stably expressing wild type rabbit RyR1, wild type Spodoptera frugiperda RyR (Sf RyR), or Sf RyR carrying different resistance mutations, including G4891E, G4891E/I4734M, and Y4867F, respectively. R-CEPIA1er, a genetically encoded fluorescent protein, was also introduced in these cell lines to report the Ca(2+) concentration in the endoplasmic reticulum. The activities of six commercial diamide insecticides were systematically characterized against different RyRs using the time-lapse fluorescence assay. Among them, cyantraniliprole (CYAN) displayed the highest activity against all three resistant Sf RyRs. The good performance of CYAN was confirmed by the toxicity assay using gene-edited Drosophila expressing the mutant RyRs, in which CYAN showed the lowest LD(50) value for the double resistant mutant. In addition, their acitivty were compared between mammalian and insect RyRs and found that flubendiamide has the best insect-selectivity. The mechanism of the anti-resistance property and selectivity of the compounds was proposed based on the structural models generated by homology modeling and molecular docking. These findings provide insights into the mechanism of insect resistance and guidance for developing effective RyR agonists that can selectively target resistant pests. |
| Scott, H., Dong, L., Stevenson, A., MacDonald, A. I., Srinivasan, S., Massimi, P., Banks, L., Martin, P. E., Johnstone, S. R. and Graham, S. V. (2023). The human discs large protein 1 interacts with and maintains connexin 43 at the plasma membrane in keratinocytes. J Cell Sci 136(11). PubMed ID: 37288673
Summary: Gap junction channels, composed of connexins, allow direct cell-to-cell communication. Connexin 43 (Cx43; also known as GJA1 for which there is no ortholog) is widely expressed in tissues, including the epidermis. In a previous study of human papillomavirus-positive cervical epithelial tumour cells, this study identified Cx43 as a binding partner of the human homologue of Drosophila Discs large (Dlg1; also known as SAP97). Dlg1 is a member of the membrane associated-guanylate kinase (MAGUK) scaffolding protein family, which is known to control cell shape and polarity. This study shows that Cx43 also interacts with Dlg1 in uninfected keratinocytes in vitro and in keratinocytes, dermal cells and adipocytes in normal human epidermis in vivo. Depletion of Dlg1 in keratinocytes did not alter Cx43 transcription but was associated with a reduction in Cx43 protein levels. Reduced Dlg1 levels in keratinocytes resulted in a reduction in Cx43 at the plasma membrane with a concomitant reduction in gap junctional intercellular communication and relocation of Cx43 to the Golgi compartment. These data suggest a key role for Dlg1 in maintaining Cx43 at the plasma membrane in keratinocytes. | Zarubin, M., Azorskaya, T., Kuldoshina, O., Alekseev, S., Mitrofanov, S. and Kravchenko, E. (2023). The tardigrade Dsup protein enhances radioresistance in Drosophila melanogaster and acts as an unspecific repressor of transcription. iScience 26(7): 106998. PubMed ID: 37534176
Summary: Tardigrades are free-living tiny invertebrates belonging to the phylum Tardigrada. They are considered to be close relatives of arthropods and worms. The tardigrade-unique damage suppressor protein (Dsup) can protect DNA from ionizing radiation and reactive oxygen species (ROS). This study generated Dsup-expressing lines of Drosophila melanogaster and demonstrated that Dsup increased the survival rate after γ-ray irradiation and hydrogen peroxide treatment in flies too, but reduced the level of their locomotor activity. The transcriptome analyses of Dsup-expressing lines revealed a significant number of differentially expressed genes, >99% of which were down-regulated. Moreover, Dsup could bind RNA. These findings suggest that Dsup can act not only as a DNA protector but also as a non-specific transcriptional repressor and RNA-binding protein, that may lead to disturbance of a number of biological processes in D. melanogaster. The obtained data demonstrate features of the Dsup protein action in non-tardigrade organisms and can be used to understand the impact of other unspecific DNA/RNA-binding proteins on ROS and radiation resistance, gene expression, and epigenetic processes. |
Tuesday, January 16th, Adult Development |
| Vuong, L. T. and Mlodzik, M. (2023). Wg/Wnt-signaling induced nuclear translocation of β-catenin is attenuated by a β-catenin peptide through its interaction with IFT-A in development and cancer cells. bioRxiv. PubMed ID: 37398005
Summary: Wnt/Wingless (Wg) signaling is critical for many developmental patterning processes and linked to diseases, including cancer. Canonical Wnt-signaling is mediated by β-catenin, Armadillo/Arm in Drosophila transducing signal activation to a nuclear response. The IFT-A/Kinesin-2 complex is required to promote the nuclear translocation of β-catenin/Arm. This study defined a small conserved N-terminal Arm/β-catenin (Arm (34-87)) peptide, which binds IFT140, as a dominant interference tool to attenuate Wg/Wnt-signaling in vivo. Expression of Arm (34-87) is sufficient to antagonize endogenous Wnt/Wg-signaling activation resulting in marked reduction of Wg-signaling target gene expression. This effect is modulated by endogenous levels of Arm and IFT140, with the Arm (34-87) effect being enhanced or suppressed, respectively. Arm (34-87) thus inhibits Wg/Wnt-signaling by interfering with the nuclear translocation of endogenous Arm/β-catenin. Importantly, this mechanism is conserved in mammals with the equivalent β-catenin (34-87) peptide blocking nuclear translocation and pathway activation, including in cancer cells. This work indicates that Wnt-signaling can be regulated by a defined N-terminal peptide of Arm/β-catenin, and thus this might serve as an entry point for potential therapeutic applications to attenuate Wnt/β-catenin signaling. | Wen, D., Chen, Z., Wen, J. and Jia, Q. (2023). Sterol Regulation of Development and 20-Hydroxyecdysone Biosynthetic and Signaling Genes in Drosophila melanogaster. Cells 12(13). PubMed ID: 37443773
Summary: Ecdysteroids are crucial in regulating the growth and development of insects. In the fruit fly Drosophila melanogaster, both C(27) and C(28) ecdysteroids have been identified. While the biosynthetic pathway of the C(27) ecdysteroid 20-hydroxyecdysone (20E) from cholesterol is relatively well understood, the biosynthetic pathway of C(28) ecdysteroids from C(28) or C(29) dietary sterols remains unknown. This study found that different dietary sterols (including the C(27) sterols cholesterol and 7-dehydrocholesterol, the C(28) sterols brassicasterol, campesterol, and ergosterol, and the C(29) sterols β-sitosterol, α-spinasterol, and stigmasterol) differentially affected the expression of 20E biosynthetic genes to varying degrees, but similarly activated 20E primary response gene expression in D. melanogaster Kc cells. It was also found that a single dietary sterol was sufficient to support D. melanogaster growth and development. Furthermore, the expression levels of some 20E biosynthetic genes were significantly altered, whereas the expression of 20E signaling primary response genes remained unaffected when flies were reared on lipid-depleted diets supplemented with single sterol types. Overall, this study provided preliminary clues to suggest that the same enzymatic system responsible for the classical C(27) ecdysteroid 20E biosynthetic pathway also participated in the conversion of C(28) and C(29) dietary sterols into C(28) ecdysteroids. |
| Williams, A. M. and Horne-Badovinac, S. (2023). Fat2 polarizes Lar and Sema5c to coordinate the motility of collectively migrating epithelial cells. J Cell Sci. PubMed ID: 37593878
Summary: Migrating epithelial cells globally align their migration machinery to achieve tissue-level movement. Biochemical signaling across leading-trailing cell-cell interfaces can promote this alignment by partitioning migratory behaviors like protrusion and retraction to opposite sides of the interface. However, how signaling proteins become organized at interfaces to accomplish this is poorly understood. The follicular epithelial cells of Drosophila melanogaster have two signaling modules at their leading-trailing interfaces-one composed of the atypical cadherin Fat2 and the receptor tyrosine phosphatase Lar, and one composed of Semaphorin5c and its receptorPlexin A. This study shows that these modules form one interface signaling system with Fat2 at its core. Trailing edge-enriched Fat2 concentrates both Lar and Semaphorin5c at cells' leading edges, but Lar and Semaphorin5c play little role in Fat2's localization. Fat2 is also more stable at interfaces than Lar and Semaphorin5c. Once localized, Lar and Semaphorin5c act in parallel to promote collective migration. It is proposed that Fat2 serves as the organizer this interface signaling system by coupling and polarizing the distributions of multiple effectors that work together to align the migration machinery of neighboring cells. | Xue, M., Cong, F., Zheng, W., Xu, R., Liu, X., Bao, H., Sung, Y. Y., Xi, Y., He, F., Ma, J., Yang, X. and Ge, W. (2023). Loss of Paip1 causes translation reduction and induces apoptotic cell death through ISR activation and Xrp1. Cell Death Discov 9(1): 288. PubMed ID: 37543696
Summary: Regulation of protein translation initiation is tightly associated with cell growth and survival. This study identified Paip1, the Drosophila homolog of the translation initiation factor PAIP1 and analyzed its role during development. Through genetic analysis, this study found that loss of Paip1 causes reduced protein translation and pupal lethality. Furthermore, tissue specific knockdown of Paip1 results in apoptotic cell death in the wing imaginal disc. Paip1 depletion leads to increased proteotoxic stress and activation of the integrated stress response (ISR) pathway. Mechanistically, it was shown that loss of Paip1 promotes phosphorylation of eIF2α via the kinase PERK, leading to apoptotic cell death. Moreover, Paip1 depletion upregulates the transcription factor gene Xrp1, which contributes to apoptotic cell death and eIF2α phosphorylation. It was further shown that loss of Paip1 leads to an increase in Xrp1 translation mediated by its 5'UTR. These findings uncover a novel mechanism that links translation impairment to tissue homeostasis and establish a role of ISR activation and Xrp1 in promoting cell death. |
| Troost, T., Binshtok, U., Sprinzak, D. and Klein, T. (2023). Cis-inhibition suppresses basal Notch signaling during sensory organ precursor selection. Proc Natl Acad Sci U S A 120(23): e2214535120. PubMed ID: 37252950
Summary: The emergence of the sensory organ precursor (SOP) from an equivalence group in Drosophila is a paradigm for studying single-cell fate specification through Notch-mediated lateral inhibition. Yet, it remains unclear how only a single SOP is selected from a relatively large group of cells. A critical aspect of SOP selection is controlled by cis-inhibition (CI), whereby the Notch ligands,Delta (Dl), cis-inhibit Notch receptors in the same cell. Based on the observation that the mammalian ligand Dl-like 1 cannot cis-inhibit Notch in Drosophila, this study probed the role of CI in vivo. A mathematical model was developed for SOP selection where Dl activity is independently regulated by the ubiquitin ligases Neuralized and Mindbomb1. This study showed theoretically and experimentally that Mindbomb1 induces basal Notch activity, which is suppressed by CI. These results highlight the trade-off between basal Notch activity and CI as a mechanism for singling out a SOP from a large equivalence group. | Yost, P. P., Al-Nouman, A. and Curtiss, J. (2023). The Rap1 small GTPase affects cell fate or survival and morphogenetic patterning during Drosophila melanogaster eye development. Differentiation 133: 12-24. PubMed ID: 37437447
Summary: The Drosophila melanogaster eye has been instrumental for determining both how cells communicate with one another to determine cell fate, as well as cell morphogenesis and patterning. This study describes the effects of the small GTPase Rap1 on the development of multiple cell types in the D. melanogaster eye. Although Rap1 has previously been linked to RTK-Ras-MAPK signaling in eye development, this study demonstrate that manipulation of Rap1 activity is modified by increase or decrease of Delta/Notch signaling during several events of cell fate specification in eye development. In addition, it was demonstrated that manipulating Rap1 function either in primary pigment cells or in interommatidial cells affects cone cell contact switching, primary pigment cell enwrapment of the ommatidial cluster, and sorting of secondary and tertiary pigment cells. These data suggest that Rap1 has roles in both ommatidial cell recruitment/survival and in ommatidial morphogenesis in the pupal stage. They lay groundwork for future experiments on the role of Rap1 in these events. |
Tuesday, January 16th - Signaling |
| Vuong, L. T. and Mlodzik, M. (2023). Wg/Wnt-signaling induced nuclear translocation of β-catenin is attenuated by a β-catenin peptide through its interaction with IFT-A in development and cancer cells. bioRxiv. PubMed ID: 37398005
Summary: Wnt/Wingless (Wg) signaling is critical for many developmental patterning processes and linked to diseases, including cancer. Canonical Wnt-signaling is mediated by β-catenin, Armadillo/Arm in Drosophila transducing signal activation to a nuclear response. The IFT-A/Kinesin-2 complex is required to promote the nuclear translocation of β-catenin/Arm. This study defined a small conserved N-terminal Arm/β-catenin (Arm (34-87)) peptide, which binds IFT140, as a dominant interference tool to attenuate Wg/Wnt-signaling in vivo. Expression of Arm (34-87) is sufficient to antagonize endogenous Wnt/Wg-signaling activation resulting in marked reduction of Wg-signaling target gene expression. This effect is modulated by endogenous levels of Arm and IFT140, with the Arm (34-87) effect being enhanced or suppressed, respectively. Arm (34-87) thus inhibits Wg/Wnt-signaling by interfering with the nuclear translocation of endogenous Arm/β-catenin. Importantly, this mechanism is conserved in mammals with the equivalent β-catenin (34-87) peptide blocking nuclear translocation and pathway activation, including in cancer cells. This work indicates that Wnt-signaling can be regulated by a defined N-terminal peptide of Arm/β-catenin, and thus this might serve as an entry point for potential therapeutic applications to attenuate Wnt/β-catenin signaling. | Wen, D., Chen, Z., Wen, J. and Jia, Q. (2023). Sterol Regulation of Development and 20-Hydroxyecdysone Biosynthetic and Signaling Genes in Drosophila melanogaster. Cells 12(13). PubMed ID: 37443773
Summary: Ecdysteroids are crucial in regulating the growth and development of insects. In the fruit fly Drosophila melanogaster, both C(27) and C(28) ecdysteroids have been identified. While the biosynthetic pathway of the C(27) ecdysteroid 20-hydroxyecdysone (20E) from cholesterol is relatively well understood, the biosynthetic pathway of C(28) ecdysteroids from C(28) or C(29) dietary sterols remains unknown. This study found that different dietary sterols (including the C(27) sterols cholesterol and 7-dehydrocholesterol, the C(28) sterols brassicasterol, campesterol, and ergosterol, and the C(29) sterols β-sitosterol, α-spinasterol, and stigmasterol) differentially affected the expression of 20E biosynthetic genes to varying degrees, but similarly activated 20E primary response gene expression in D. melanogaster Kc cells. It was also found that a single dietary sterol was sufficient to support D. melanogaster growth and development. Furthermore, the expression levels of some 20E biosynthetic genes were significantly altered, whereas the expression of 20E signaling primary response genes remained unaffected when flies were reared on lipid-depleted diets supplemented with single sterol types. Overall, this study provided preliminary clues to suggest that the same enzymatic system responsible for the classical C(27) ecdysteroid 20E biosynthetic pathway also participated in the conversion of C(28) and C(29) dietary sterols into C(28) ecdysteroids. |
| Williams, A. M. and Horne-Badovinac, S. (2023). Fat2 polarizes Lar and Sema5c to coordinate the motility of collectively migrating epithelial cells. J Cell Sci. PubMed ID: 37593878
Summary: Migrating epithelial cells globally align their migration machinery to achieve tissue-level movement. Biochemical signaling across leading-trailing cell-cell interfaces can promote this alignment by partitioning migratory behaviors like protrusion and retraction to opposite sides of the interface. However, how signaling proteins become organized at interfaces to accomplish this is poorly understood. The follicular epithelial cells of Drosophila melanogaster have two signaling modules at their leading-trailing interfaces-one composed of the atypical cadherin Fat2 and the receptor tyrosine phosphatase Lar, and one composed of Semaphorin5c and its receptorPlexin A. This study shows that these modules form one interface signaling system with Fat2 at its core. Trailing edge-enriched Fat2 concentrates both Lar and Semaphorin5c at cells' leading edges, but Lar and Semaphorin5c play little role in Fat2's localization. Fat2 is also more stable at interfaces than Lar and Semaphorin5c. Once localized, Lar and Semaphorin5c act in parallel to promote collective migration. It is proposed that Fat2 serves as the organizer this interface signaling system by coupling and polarizing the distributions of multiple effectors that work together to align the migration machinery of neighboring cells. | Xue, M., Cong, F., Zheng, W., Xu, R., Liu, X., Bao, H., Sung, Y. Y., Xi, Y., He, F., Ma, J., Yang, X. and Ge, W. (2023). Loss of Paip1 causes translation reduction and induces apoptotic cell death through ISR activation and Xrp1. Cell Death Discov 9(1): 288. PubMed ID: 37543696
Summary: Regulation of protein translation initiation is tightly associated with cell growth and survival. This study identified Paip1, the Drosophila homolog of the translation initiation factor PAIP1 and analyzed its role during development. Through genetic analysis, this study found that loss of Paip1 causes reduced protein translation and pupal lethality. Furthermore, tissue specific knockdown of Paip1 results in apoptotic cell death in the wing imaginal disc. Paip1 depletion leads to increased proteotoxic stress and activation of the integrated stress response (ISR) pathway. Mechanistically, it was shown that loss of Paip1 promotes phosphorylation of eIF2α via the kinase PERK, leading to apoptotic cell death. Moreover, Paip1 depletion upregulates the transcription factor gene Xrp1, which contributes to apoptotic cell death and eIF2α phosphorylation. It was further shown that loss of Paip1 leads to an increase in Xrp1 translation mediated by its 5'UTR. These findings uncover a novel mechanism that links translation impairment to tissue homeostasis and establish a role of ISR activation and Xrp1 in promoting cell death. |
| Troost, T., Binshtok, U., Sprinzak, D. and Klein, T. (2023). Cis-inhibition suppresses basal Notch signaling during sensory organ precursor selection. Proc Natl Acad Sci U S A 120(23): e2214535120. PubMed ID: 37252950
Summary: The emergence of the sensory organ precursor (SOP) from an equivalence group in Drosophila is a paradigm for studying single-cell fate specification through Notch-mediated lateral inhibition. Yet, it remains unclear how only a single SOP is selected from a relatively large group of cells. A critical aspect of SOP selection is controlled by cis-inhibition (CI), whereby the Notch ligands, elta (Dl), cis-inhibit Notch receptors in the same cell. Based on the observation that the mammalian ligand Dl-like 1 cannot cis-inhibit Notch in Drosophila, this study probed the role of CI in vivo. A mathematical model was developed for SOP selection where Dl activity is independently regulated by the ubiquitin ligases Neuralized and Mindbomb1. This study showed theoretically and experimentally that Mindbomb1 induces basal Notch activity, which is suppressed by CI. These results highlight the trade-off between basal Notch activity and CI as a mechanism for singling out a SOP from a large equivalence group. | Yost, P. P., Al-Nouman, A. and Curtiss, J. (2023). The Rap1 small GTPase affects cell fate or survival and morphogenetic patterning during Drosophila melanogaster eye development. Differentiation 133: 12-24. PubMed ID: 37437447
Summary: The Drosophila melanogaster eye has been instrumental for determining both how cells communicate with one another to determine cell fate, as well as cell morphogenesis and patterning. This study describes the effects of the small GTPase Rap1 on the development of multiple cell types in the D. melanogaster eye. Although Rap1 has previously been linked to RTK-Ras-MAPK signaling in eye development, this study demonstrate that manipulation of Rap1 activity is modified by increase or decrease of Delta/Notch signaling during several events of cell fate specification in eye development. In addition, it was demonstrated that manipulating Rap1 function either in primary pigment cells or in interommatidial cells affects cone cell contact switching, primary pigment cell enwrapment of the ommatidial cluster, and sorting of secondary and tertiary pigment cells. These data suggest that Rap1 has roles in both ommatidial cell recruitment/survival and in ommatidial morphogenesis in the pupal stage. They lay groundwork for future experiments on the role of Rap1 in these events. |
Friday, January 11th - Behaviors |
| Xie, S. M., Lai, J. X., Liu, C. Q., Zhang, X. X., Lin, Y. M., Lan, Q. W., Hong, D. Y., Chen, X. C., Qiao, J. D. and Mao, Y. L. (2023). UBR4 deficiency causes male sterility and testis abnormal in Drosophila. Front Endocrinol (Lausanne) 14: 1165825. PubMed ID: 37529615
Summary: It has been established that UBR4 encodes E3 ubiquitin ligase, which determines the specificity of substrate binding during protein ubiquitination and has been associated with various functions of the nervous system but not the reproductive system. This study explored the role of UBR4 on fertility with a Drosophila model. Different Ubr4 knockdown flies were established using the UAS/GAL4 activating sequence system. Fertility, hatchability, and testis morphology were studied, and bioinformatics analyses were conducted. The results indicated that UBR4 deficiency could induce male sterility and influent egg hatchability in Drosophila. Ubr4 deficiency affected the testis during morphological analysis. Proteomics analysis indicated 188 upregulated proteins and 175 downregulated proteins in the testis of Ubr4 knockdown flies. Gene Ontology analysis revealed significant upregulation of CG11598 and Sfp65A, and downregulation of Pelota in Ubr4 knockdown flies. These proteins were involved in the biometabolic or reproductive process in Drosophila. These regulated proteins are important in testis generation and sperm storage promotion. Bioinformatics analysis verified that expression of UBR4 was low in cryptorchidism patients, which further supported the important role of UBR4 in male fertility. Overall, these findings suggest that UBR4 deficiency could promote male infertility and may be involved in the protein modification of UBR4 by upregulating Sfp65A and CG11598, whereas downregulating Pelota protein expression. | Salim, S., Hussain, S., Banu, A., Gowda, S. B. M., Ahammad, F., Alwa, A., Pasha, M. and Mohammad, F. (2023). The ortholog of human ssDNA-binding protein SSBP3 influences neurodevelopment and autism-like behaviors in Drosophila melanogaster. PLoS Biol 21(7): e3002210. PubMed ID: 37486945
Summary: The 1p32.3 microdeletion is implicated in many neurodevelopmental disorders. One deleted gene is the single-stranded DNA-binding protein 3 (SSBP3); its Drosophila ortholog is Ssdp). This study investigated consequences of Ssdp manipulations. SSBP3 and Ssdp are expressed in excitatory neurons in the brain. Ssdp overexpression caused morphological alterations in Drosophila wing, mechanosensory bristles, and head. Ssdp manipulations also affected the neuropil brain volume and glial cell number in larvae and adult flies. Moreover, Ssdp overexpression led to differential changes in synaptic density in specific brain regions. Decreased levels of armadillo were observed in the heads of Ssdp overexpressing flies, as well as a decrease in armadillo and wingless expression in the larval wing discs, implicating the involvement of the canonical Wnt signaling pathway in Ssdp function. RNA sequencing revealed perturbation of oxidative stress-related pathways in heads of Ssdp overexpressing flies. Furthermore, Ssdp overexpressing brains showed enhanced reactive oxygen species (ROS) and altered neuronal mitochondrial morphology. Flies with elevated levels of Ssdp exhibited behavior defects, which were phenocopied in pan-neuronal Ssdp knockdown flies, suggesting that Ssdp is dosage sensitive. Notably, Ssdp knockdown exclusively in adult flies did not produce behavioral and functional defects. Finally, optogenetic manipulation of Ssdp-expressing neurons altered autism-associated behaviors. This study proposes SSBP3 as a critical gene in the 1p32.3 microdeletion/duplication genomic region and sheds light on the functional role of Ssdp in neurodevelopmental processes in Drosophila. |
| Sun, Z., Nystul, T. G. and Zhong, G. (2023). Single-cell RNA sequencing identifies eggplant as a regulator of germ cell development in Drosophila. EMBO Rep: e56475. PubMed ID: 37603128
Drosophila ovarian germline stem cells (GSCs) are a powerful model for stem cell research. In this study, single-cell RNA sequencing (scRNA-seq), an RNAi screen and bioinformatic analysis, was used to identify genes involved in germ cell differentiation, including 34 genes with upregulated expression during early germ cell development and 19 genes that may regulate germ cell differentiation. Among these, a gene named eggplant (eggpl - CG32814) is highly expressed in GSCs and downregulated in early daughter cells. RNAi knockdown of eggpl causes germ cell proliferation and differentiation defects. In flies fed a rich yeast diet, the expression of eggpl is significantly lower and knockdown or knockout of eggpl phenocopies a rich diet. In addition, eggpl knockdown suppresses the reduction in germ cell proliferation caused by inhibition of the insulin effector PI3K. These findings suggest that downregulation of eggpl links nutritional status to germ cell proliferation and differentiation. Collectively, this study provides new insights into the signaling networks that regulate early germ cell development and identifies eggpl as a key player in this process. | Roy, S. D., Nagarajan, S., Jalal, M. S., Basar, M. A. and Duttaroy, A. (2023). New mutant alleles for Spargel/dPGC-1 highlights the function of Spargel RRM domain in oogenesis and expands the role of Spargel in embryogenesis and intracellular transport. G3 (Bethesda). PubMed ID: 37369430
Summary: Energy metabolism in vertebrates is controlled by three members of the PGC-1 (PPAR γ- coactivator 1) family, transcriptional coactivators that shape responses to physiological stimuli by interacting with the nuclear receptors and other transcription factors. Multiple evidence now supports that Spargel protein found in insects and ascidians is the ancestral form of vertebrate PGC-1's. This study undertook functional analysis of srl gene in Drosophila, asking about the requirement of Spargel per se during embryogenesis and its RNA binding domains. CRISPR- engineered srl gene deletion turned out to be an amorphic allele that is late embryonic/early larval lethal and Spargel protein missing its RNA binding domain (SrlΔRRM) negatively affects female fertility. Overexpression of wild-type Spargel in transgenic flies expedited the growth of egg chambers. On the other hand, oogenesis is blocked in a dominant-negative fashion in the presence of excess Spargel lacking its RRM domains. Finally, aggregation of Notch proteins was observed in egg chambers of srl mutant flies, suggesting that Spargel is involved in intracellular transport of Notch proteins. Taken together, this study claims that these new mutant alleles of spargel are emerging powerful tools for revealing new biological functions for Spargel, an essential transcription coactivator in both Drosophila and mammals. |
| Wooten, M., Takushi, B., Ahmad, K. and Henikoff, S. (2023).. Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters. Sci Adv 9(24): eadg3257. PubMed ID: 37315134
Anthracyclines are a class of widely prescribed anticancer drugs that disrupt chromatin by intercalating into DNA and enhancing nucleosome turnover. To understand the molecular consequences of anthracycline-mediated chromatin disruption, Cleavage Under Targets and Tagmentation (CUT&Tag) was used to profile RNA polymerase II during anthracycline treatment in Drosophila cells. Treatment with the anthracycline aclarubicin leads to elevated levels of RNA polymerase II and changes in chromatin accessibility. It was found that promoter proximity and orientation affect chromatin changes during aclarubicin treatment, as closely spaced divergent promoter pairs show greater chromatin changes when compared to codirectionally oriented tandem promoters. It was also found that aclarubicin treatment changes the distribution of noncanonical DNA G-quadruplex structures both at promoters and at G-rich pericentromeric repeats. This work suggests that the cancer-killing activity of aclarubicin is driven by the disruption of nucleosomes and RNA polymerase II. | Vdovina, Y. A., Kurshakova, M. M., Georgieva, S. G. and Kopytova, D. V. (2023). PCID2 Subunit of the Drosophila TREX-2 Complex Has Two RNA-Binding Regions. Curr Issues Mol Biol 45(7): 5662-5676. PubMed ID: 37504273
Summary: Drosophila PCID2 is a subunit of the TREX-2 mRNA nuclear export complex. Although the complex has long been studied in eukaryotes, it is still unclear how TREX-2 interacts with mRNA in multicellular organisms. Here, the interaction between Drosophila PCID2 and the ras2 RNA was studied by EMSA. The C-terminal region of the WH domain of PCID2 specifically binds the 3'-noncoding region of the ras2 RNA. While the same region of PCID2 interacts with the Xmas-2 subunit of the TREX-2 complex, PCID2 interacts with RNA independently of Xmas-2. An additional RNA-binding region (M region) was identified in the N-terminal part of the PCI domain and found to bind RNA nonspecifically. Point mutations of evolutionarily conserved amino acid residues in this region completely abolish the PCID2-RNA interaction, while a deletion of the C-terminal domain only partly decreases it. Thus, the specific interaction of PCID2 with RNA requires nonspecific PCID2-RNA binding. |
Wednesday, January 10th - Chromatin |
| Tolokh, I. S., Kinney, N. A., Sharakhov, I. V. and Onufriev, A. V. (2023). Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin. Epigenetics Chromatin 16(1): 21. PubMed ID: 37254161
Summary: Interactions among topologically associating domains (TADs), and between the nuclear envelope (NE) and lamina-associated domains (LADs) are expected to shape various aspects of three-dimensional (3D) chromatin structure and dynamics. This study has developed a dynamical model of D. melanogaster nuclei at TAD resolution that explicitly accounts for four distinct epigenetic classes of TADs and LAD-NE interactions. The model is parameterized to reproduce the experimental Hi-C map of the wild type (WT) nuclei; it describes time evolution of the chromatin over the G1 phase of the interphase. Predicted positioning of all LADs at the NE is highly dynamic-the same LAD can attach, detach and move far away from the NE multiple times during interphase. The probabilities of LADs to be in contact with the NE vary by an order of magnitude, despite all having the same affinity to the NE in the model. These probabilities are mostly determined by a highly variable local linear density of LADs along the genome, which also has the same strong effect on the predicted positioning of individual TADs -- higher probability of a TAD to be near NE is largely determined by a higher linear density of LADs surrounding this TAD. The distribution of LADs along the chromosome chains plays a notable role in maintaining a non-random average global structure of chromatin. Relatively high affinity of LADs to the NE in the WT nuclei substantially reduces sensitivity of the global radial chromatin distribution to variations in the strength of TAD-TAD interactions compared to the lamin depleted nuclei, where a small (0.5 kT) increase of cross-type TAD-TAD interactions doubles the chromatin density in the central nucleus region. A dynamical model of the entire fruit fly genome makes multiple genome-wide predictions of biological interest. The distribution of LADs along the chromatin chains affects their probabilities to be in contact with the NE and radial positioning of highly mobile TADs, playing a notable role in creating a non-random average global structure of the chromatin. It is conjectured that an important role of attractive LAD-NE interactions is to stabilize global chromatin structure against inevitable cell-to-cell variations in TAD-TAD interactions. | Tortora, M. M. C., Brennan, L. D., Karpen, G. and Jost, D. (2023). HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation. Proc Natl Acad Sci U S A 120(33): e2211855120. PubMed ID: 37549295
Summary: The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-less nuclear compartments involves the binding of Heterochromatin Protein 1 (HP1) to H3K9me2/3-rich genomic regions. While HP1 exhibits liquid-liquid phase separation properties in vitro, its mechanistic impact on the structure and dynamics of PCH condensate formation in vivo remains largely unresolved. Using a minimal theoretical framework, this study systematically investigate the mutual coupling between self-interacting HP1-like molecules and the chromatin polymer. The specific affinity of HP1 for H3K9me2/3 loci was shown to facilitate coacervation in nucleo and promotes the formation of stable PCH condensates at HP1 levels far below the concentration required to observe phase separation in purified protein assays in vitro. These heterotypic HP1-chromatin interactions give rise to a strong dependence of the nucleoplasmic HP1 density on HP1-H3K9me2/3 stoichiometry, consistent with the thermodynamics of multicomponent phase separation. The dynamical cross talk between HP1 and the viscoelastic chromatin scaffold also leads to anomalously slow equilibration kinetics, which strongly depend on the genomic distribution of H3K9me2/3 domains and result in the coexistence of multiple long-lived, microphase-separated PCH compartments. The morphology of these complex coacervates is further found to be governed by the dynamic establishment of the underlying H3K9me2/3 landscape, which may drive their increasingly abnormal, aspherical shapes during cell development. These findings compare favorably to 4D microscopy measurements of HP1 condensate formation in live Drosophila embryos and suggest a general quantitative model of PCH formation based on the interplay between HP1-based phase separation and chromatin polymer mechanics. |
| Prozzillo, Y., Fattorini, G., Ferreri, D., Leo, M., Dimitri, P. and Messina, G. (2023). Knockdown of DOM/Tip60 Complex Subunits Impairs Male Meiosis of Drosophila melanogaster. Cells 12(10). PubMed ID: 37408183
Summary: ATP-dependent chromatin remodeling complexes are involved in nucleosome sliding and eviction and/or the incorporation of histone variants into chromatin to facilitate several cellular and biological processes, including DNA transcription, replication and repair. The DOM/TIP60 chromatin remodeling complex of Drosophila melanogaster contains 18 subunits, including DOMINO (DOM), an ATPase that catalyzes the exchange of the canonical H2A with its variant (H2A.V), and TIP60, a lysine-acetyltransferase that acetylates H4, H2A and H2A.V histones. In recent decades, experimental evidence has shown that ATP-dependent chromatin remodeling factors, in addition to their role in chromatin organization, have a functional relevance in cell division. In particular, emerging studies suggested the direct roles of ATP-dependent chromatin remodeling complex subunits in controlling mitosis and cytokinesis in both humans and D. melanogaster. However, little is known about their possible involvement during meiosis. The results of this work show that the knockdown of 12 of DOM/TIP60 complex subunits generates cell division defects that, in turn, cause total/partial sterility in Drosophila males, providing new insights into the functions of chromatin remodelers in cell division control during gametogenesis. | Rajan, A., Anhezini, L., Rives-Quinto, N., Chhabra, J. Y., Neville, M. C., Larson, E. D., Goodwin, S. F., Harrison, M. M. and Lee, C. Y. (2023). Low-level repressive histone marks fine-tune gene transcription in neural stem cells. PubMed ID: 37314324
Summary: Coordinated regulation of gene activity by transcriptional and translational mechanisms poise stem cells for a timely cell-state transition during differentiation. Although important for all stemness-to-differentiation transitions, mechanistic understanding of the fine-tuning of gene transcription is lacking due to the compensatory effect of translational control. This study used intermediate neural progenitor (INP) identity commitment to define the mechanisms that fine-tune stemness gene transcription in fly neural stem cells (neuroblasts). This study demonstrated that the transcription factor Fruitless(C) (Fru(C)) binds cis-regulatory elements of most genes uniquely transcribed in neuroblasts. Loss of fru(C) function alone has no effect on INP commitment but drives INP dedifferentiation when translational control is reduced. Fru(C) negatively regulates gene expression by promoting low-level enrichment of the repressive histone mark H3K27me3 in gene cis-regulatory regions. Identical to fru(C) loss-of-function, reducing Polycomb Repressive Complex 2 activity increases stemness gene activity. It is proposed that low-level H3K27me3 enrichment fine-tunes gene transcription in stem cells, a mechanism likely conserved from flies to humans. |
| Tang, M., Regadas, I., Belikov, S., Shilkova, O., Xu, L., Wernersson, E., Liu, X., Wu, H., Bienko, M. and Mannervik, M. (2023). Separation of transcriptional repressor and activator functions in Drosophila HDAC3. Development 150(15). PubMed ID: 37455638
Summary: The histone deacetylase HDAC3 is associated with the NCoR/SMRT co-repressor complex, and its canonical function is in transcriptional repression, but it can also activate transcription. This study shows that the repressor and activator functions of HDAC3 can be genetically separated in Drosophila. A lysine substitution in the N terminus (K26A) disrupts its catalytic activity and activator function, whereas a combination of substitutions (HEBI) abrogating the interaction with SMRTER enhances repressor activity beyond wild type in the early embryo. It is concluded that the crucial functions of HDAC3 in embryo development involve catalytic-dependent gene activation and non-enzymatic repression by several mechanisms, including tethering of loci to the nuclear periphery. | Williamson, I., Boyle, S., Grimes, G. R., Friman, E. T. and Bickmore, W. A. (2023). Dispersal of PRC1 condensates disrupts polycomb chromatin domains and loops. Life Sci Alliance 6(10). PubMed ID: 37487640
Summary: Polycomb repressive complex 1 (PRC1) strongly influences 3D genome organization, mediating local chromatin compaction and clustering of target loci. Several PRC1 subunits have the capacity to form biomolecular condensates through liquid-liquid phase separation in vitro and when tagged and over-expressed in cells. This study used 1,6-hexanediol, which can disrupt liquid-like condensates, to examine the role of endogenous PRC1 biomolecular condensates on local and chromosome-wide clustering of PRC1-bound loci. Using imaging and chromatin immunoprecipitation, this study showed that PRC1-mediated chromatin compaction and clustering of targeted genomic loci-at different length scales-can be reversibly disrupted by the addition and subsequent removal of 1,6-hexanediol to mouse embryonic stem cells. Decompaction and dispersal of polycomb domains and clusters cannot be solely attributable to reduced PRC1 occupancy detected by chromatin immunoprecipitation following 1,6-hexanediol treatment as the addition of 2,5-hexanediol has similar effects on binding despite this alcohol not perturbing PRC1-mediated 3D clustering, at least at the sub-megabase and megabase scales. These results suggest that weak hydrophobic interactions between PRC1 molecules may have a role in polycomb-mediated genome organization. |
Monday, January 8th - Stress |
| Wen, D., Xie, J., Yuan, Y., Shen, L., Yang, Y. and Chen, W. (2023). The endogenous antioxidant ability of royal jelly in Drosophila is independent of Keap1/Nrf2 by activating oxidoreductase activity. Insect Sci. PubMed ID: 37632209
Summary: Royal jelly (RJ) is a biologically active substance secreted by the hypopharyngeal and mandibular glands of worker honeybees. It is widely claimed that RJ reduces oxidative stress. However, the antioxidant activity of RJ has mostly been determined by in vitro chemical detection methods or by external administration drugs that cause oxidative stress. Whether RJ can clear the endogenous production of reactive oxygen species (ROS) in cells remains largely unknown. This study systematically investigated the antioxidant properties of RJ using several endogenous oxidative stress models of Drosophila. RJ was found to enhance sleep quality of aging Drosophila, which is decreased due to an increase of oxidative damage with age. RJ supplementation improved survival and suppressed ROS levels in gut cells of flies upon exposure to hydrogen peroxide or to the neurotoxic agent paraquat. Moreover, RJ supplementation moderated levels of ROS in endogenous gut cells and extended lifespan after exposure of flies to heat stress. Sleep deprivation leads to accumulation of ROS in the gut cells, and RJ attenuated the consequences of oxidative stress caused by sleep loss and prolonged lifespan. Mechanistically, RJ prevented cell oxidative damage caused by heat stress or sleep deprivation, with the antioxidant activity in vivo independent of Keap1/Nrf2 signaling. RJ supplementation activated oxidoreductase activity in the guts of flies, suggesting its ability to inhibit endogenous oxidative stress and maintain health, possibly in humans. | Kiparaki, M. and Baker, N. E. (2023). Ribosomal protein mutations and cell competition: autonomous and nonautonomous effects on a stress response. Genetics 224(3). PubMed ID: 37267156
Summary: Ribosomal proteins (Rps) are essential for viability. Genetic mutations affecting Rp genes were first discovered in Drosophila, where they represent a major class of haploinsufficient mutations. One mutant copy gives rise to the dominant "Minute" phenotype, characterized by slow growth and small, thin bristles. Wild-type (WT) and Minute cells compete in mosaics, that is, Rp+/- are preferentially lost when their neighbors are of the wild-type genotype. Many features of Rp gene haploinsufficiency (i.e. Rp+/- phenotypes) are mediated by a transcriptional program. In Drosophila, reduced translation and slow growth are under the control of Xrp1, a bZip-domain transcription factor induced in Rp mutant cells that leads ultimately to the phosphorylation of eIF2α; and consequently inhibition of most translation. Rp mutant phenotypes are also mediated transcriptionally in yeast and in mammals. In mammals, the Impaired Ribosome Biogenesis Checkpoint activates p53. Recent findings link Rp mutant phenotypes to other cellular stresses, including the DNA damage response and endoplasmic reticulum stress. It is suggested that cell competition results from nonautonomous inputs to stress responses, bringing decisions between adaptive and apoptotic outcomes under the influence of nearby cells. In Drosophila, cell competition eliminates aneuploid cells in which loss of chromosome leads to Rp gene haploinsufficiency. The effects of Rp gene mutations on the whole organism, in Minute flies or in humans with Diamond-Blackfan Anemia, may be inevitable consequences of pathways that are useful in eliminating individual cells from mosaics. Alternatively, apparently deleterious whole organism phenotypes might be adaptive, preventing even more detrimental outcomes. In mammals, for example, p53 activation appears to supress oncogenic effects of Rp gene haploinsufficiency. |
| Krama, T., Bahhir, D., Ots, L., Popovs, S., Bartkevics, V., Pugajeva, I., Krams, R., Merivee, E., Must, A., Rantala, M. J., Krams, I. and Joers, P. (2023). A diabetes-like biochemical and behavioural phenotype of Drosophila induced by predator stress. Proc Biol Sci 290(2002): 20230442. PubMed ID: 37403506
Summary: Predation can have both lethal and non-lethal effects on prey. The non-lethal effects of predation can instil changes in prey life history, behaviour, morphology and physiology, causing adaptive evolution. The chronic stress caused by sustained predation on prey is comparable to chronic stress conditions in humans. Conditions like anxiety, depression, and post-traumatic stress syndrome have also been implicated in the development of metabolic disorders such as obesity and diabetes. This study found that predator stress induced during larval development in fruit flies Drosophila melanogaster impairs carbohydrate metabolism by systemic inhibition of Akt protein kinase, which is a central regulator of glucose uptake. However, Drosophila grown with predators survived better under direct spider predation in the adult phase. Administration of metformin and 5-hydroxytryptophan (5-HTP), a precursor of the neurotransmitter serotonin, reversed these effects. These results demonstrate a direct link between predator stress and metabolic impairment, suggesting that a diabetes-like biochemical phenotype may be adaptive in terms of survival and reproductive success. This study provides a novel animal model to explore the mechanisms responsible for the onset of these metabolic disorders, which are highly prevalent in human populations. | Lidsky, P. V., Yuan, J., Lashkevich, K. A., Dmitriev, S. E. and Andino, R. (2023). Monitoring integrated stress response in live Drosophila. bioRxiv. PubMed ID: 37502856
Summary: Cells exhibit stress responses to various environmental changes. Among these responses, the integrated stress response (ISR) plays a pivotal role as a crucial stress signaling pathway. While extensive ISR research has been conducted on cultured cells, understanding of its implications in multicellular organisms remains limited, largely due to the constraints of current techniques that hinder the ability to track and manipulate the ISR in vivo. To overcome these limitations, this study has successfully developed an internal ribosome entry site (IRES)-based fluorescent reporter system. This innovative reporter enables labelling of Drosophila cells, within the context of a living organism, that exhibit eIF2 phosphorylation-dependent translational shutoff - a characteristic feature of the ISR and viral infections. Through this methodology, this study has unveiled tissue- and cell-specific regulation of stress response in Drosophila flies and have even been able to detect stressed tissues in vivo during virus and bacterial infections. To further validate the specificity of the reporter, this study has engineered ISR-null eIF2αS50A mutant flies for stress response analysis. The results shed light on the tremendous potential of this technique for investigating a broad range of developmental, stress, and infection-related experimental conditions. Combining the reporter tool with ISR-null mutants establishes Drosophila as an exceptionally powerful model for studying the ISR in the context of multicellular organisms. |
| Hu, D., Li, W., Wang, J., Peng, Y., Yun, Y. and Peng, Y. (2023). Interaction of High Temperature stress and Wolbachia Infection on the Biological Characteristic of Drosophila melanogaster. Insects 14(6). PubMed ID: 37367374
Summary: It was reported that temperature affects the distribution of Wolbachia in the host, but only a few papers reported the effect of the interaction between high temperature and Wolbachia on the biological characteristic of the host. This study found four treatment Drosophila melanogaster groups: Wolbachia-infected flies in 25 °C (W(+)M), Wolbachia-infected flies in 31 °C (W(+)H), Wolbachia-uninfected flies in 25 °C (W(-)M), Wolbachia-uninfected flies in 31 °C (W(-)H), and the interaction effect of temperature and Wolbachia infection on the biological characteristic of D. melanogaster in F(1), F(2) and F(3) generations was detected. Both temperature and Wolbachia infection had significant effects on the development and survival rate of D. melanogaster. High temperature and Wolbachia infection had interaction effect on hatching rate, developmental durations, emergence rate, body weight and body length of F(1), F(2) and F(3) flies, and the interaction effect also existed on oviposition amount of F(3) flies, and on pupation rate of F(2) and F(3) flies. High temperature stress reduced the Wolbachia vertical transmission efficiency between generations. These results indicated that high temperature stress and Wolbachia infection had negative effects on the morphological development of D. melanogaster. | Li, X., Li, M., Xue, X. and Wang, X. (2023). Proteomic analysis reveals oxidative stress-induced activation of Hippo signaling in thiamethoxam-exposed Drosophila. Chemosphere 338: 139448. PubMed ID: 37437626
Summary: Thiamethoxam (THIA) is a widely used neonicotinoid insecticide. However, the toxicity and defense mechanisms activated in THIA-exposed insects are unclear. This study used isobaric tags for relative and absolute quantitation (iTRAQ) proteomics technology to identify changes in protein expression in THIA-exposed Drosophila. It was found that the antioxidant proteins Cyp6a23 and Dys were upregulated, whereas vir-1 was downregulated, which may have been detoxification in response to THIA exposure. Prx5 downregulation promoted the generation of reactive oxygen species. Furthermore, the accumulation of reactive oxygen species led to the induction of antioxidant defenses in THIA-exposed Drosophila, thereby enhancing the levels of oxidative stress markers (e.g., superoxide dismutase, glutathione S-transferase, and glutathione) and reducing catalase expression. Furthermore, the Hippo signaling transcription coactivator Yki was inactivated by THIA. Thise results suggesting that Hippo signaling may be necessary to promote insect survival in response to neonicotinoid insecticide toxicity. |
Thursday, January 4th - Synapse, ER, and Vesicles |
| Sung, H. and Lloyd, T. E. (2023). Disrupted endoplasmic reticulum-mediated autophagosomal biogenesis in a Drosophila model of C9-ALS-FTD. Autophagy. PubMed ID: 37599467
Summary: Macroautophagy/autophagy is a major pathway for the clearance of protein aggregates and damaged organelles, and multiple intracellular organelles participate in the process of autophagy, from autophagosome formation to maturation and degradation. Dysregulation of the autophagy pathway has been implicated in the pathogenesis of neurodegenerative diseases including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), however the mechanisms underlying autophagy impairment in these diseases are incompletely understood. Since the expansion of GGGGCC (G(4)C(2)) repeats in the first intron of the C9orf72 gene is the most common inherited cause of both ALS and FTD (C9-ALS-FTD), this study investigated autophagosome dynamics in Drosophila motor neurons expressing 30 G(4)C(2) repeats (30 R). In vivo imaging demonstrates that expression of expanded G(4)C(2) repeats markedly impairs biogenesis of autophagosomes at synaptic termini, whereas trafficking and maturation of axonal autophagosomes are unaffected. Motor neurons expressing 30 R display marked disruption in endoplasmic reticulum (ER) structure and dynamics in the soma, axons, and synapses. Disruption of ER morphology with mutations in Rtnl1 (Reticulon-like 1) or atl (atlastin) also impairs autophagosome formation in motor neurons, suggesting that ER integrity is critical for autophagosome formation. Furthermore, live imaging demonstrates that autophagosomes are generated from dynamic ER tubules at synaptic boutons, and this process fails to occur in a C9-ALS-FTD model. Together, these findings suggest that dynamic ER tubules are required for formation of autophagosomes at the neuromuscular junction, and that this process is disrupted by expanded G(4)C(2) repeats that cause ALS-FTD. | Yang, M., Zinkgraf, M., Fitzgerald-Cook, C., Harrison, B. R., Putzier, A., Promislow, D. E. L. and Wang, A. M. (2023). Using Drosophila to identify naturally occurring genetic modifiers of Aβ42- and tau-induced toxicity. G3 (Bethesda). PubMed ID: 37311212
Summary: Alzheimer's disease (AD) is characterized by two pathological proteins, amyloid beta 42 (Aβ42) and tau. The majority of AD cases in the population are sporadic and late-onset AD (LOAD), which exhibits high levels of heritability. While several genetic risk factors for LOAD have been identified and replicated in independent studies, including the ApoE ε4 allele, the great majority of the heritability of LOAD remains unexplained, likely due to the aggregate effects of a very large number of genes with small effect size, as well as to biases in sample collection and statistical approaches. This study presents an unbiased forward genetic screen in Drosophila looking for naturally occurring modifiers of Aβ42- and tau-induced ommatidial degeneration. The results identify 14 significant SNPs, which map to 12 potential genes in 8 unique genomic regions. These hits that are significant after genome-wide correction identify genes involved in neuronal development, signal transduction and organismal development. Looking more broadly at suggestive hits (P < 10-5), significant enrichment was seen in genes associated with neurogenesis, development and growth as well as significant enrichment in genes whose orthologs have been identified as significantly or suggestively associated with AD in human GWAS studies. These latter genes include ones whose orthologs are in close proximity to regions in the human genome that are associated with AD, but where a causal gene has not been identified. Together, these results illustrate the potential for complementary and convergent evidence provided through multi-trait GWAS in Drosophila to supplement and inform human studies, helping to identify the remaining heritability and novel modifiers of complex diseases. |
| Sharma, A., Narasimha, K., Manjithaya, R. and Sheeba, V. (2023). Restoration of Sleep and Circadian Behavior by Autophagy Modulation in Huntington's Disease. J Neurosci 43(26): 4907-4925. PubMed ID: 37268416
Summary: Circadian and sleep defects are well documented in Huntington's disease (HD). Modulation of the autophagy pathway has been shown to mitigate toxic effects of mutant Huntingtin (HTT) protein. However, it is not clear whether autophagy induction can also rescue circadian and sleep defects. Using a genetic approach, this study expressed human mutant HTT protein in a subset of Drosophila circadian neurons and sleep center neurons. In this context, the contribution was examined of autophagy in mitigating toxicity caused by mutant HTT protein. Targeted overexpression of an autophagy gene, Atg8a in male flies, induces autophagy pathway and partially rescues several HTT-induced behavioral defects, including sleep fragmentation, a key hallmark of many neurodegenerative disorders. Using cellular markers and genetic approaches, it was demonstrated that indeed the autophagy pathway is involved in behavioral rescue. Surprisingly, despite behavioral rescue and evidence for the involvement of the autophagy pathway, the large visible aggregates of mutant HTT protein were not eliminated. The rescue in behavior is associated with increased mutant protein aggregation and possibly enhanced output from the targeted neurons, resulting in the strengthening of downstream circuits. Overall, this study suggests that, in the presence of mutant HTT protein, Atg8a induces autophagy and improves the functioning of circadian and sleep circuits. | Tan, F. H. P., Ting, A. C. J., Najimudin, N., Watanabe, N., Shamsuddin, S., Zainuddin, A., Osada, H. and Azzam, G. (2023). 3-[[(3S)-1,2,3,4-Tetrahydroisoquinoline-3-carbonyl]amino]propanoic acid (THICAPA) is protective against Aβ42-induced toxicity in vitro and in an Alzheimer's Disease Drosophila. J Gerontol A Biol Sci Med Sci. PubMed ID: 37453137
Summary: Alzheimer's disease (AD) is the most prevalent type of dementia globally. The accumulation of amyloid-beta (Aβ) extracellular senile plaques in the brain is one of the hallmark mechanisms found in AD. Aβ42 is the most damaging and aggressively aggregating Aβ isomer produced in the brain. Although Aβ42 has been extensively researched as a crucial peptide connected to the development of the characteristic amyloid fibrils in AD, the specifics of its pathophysiology are still unknown. Therefore, the main objective was to identify novel compounds that could potentially mitigate the negative effects of Aβ42. 3-[[(3S)-1,2,3,4-Tetrahydroisoquinoline-3-carbonyl]amino]propanoic acid (THICAPA) was identified as a ligand for Aβ42 and for reducing fibrillary Aβ42 aggregation. THICAPA also improved cell viability when administered to PC12 neuronal cells that were exposed to Aβ42. Additionally, this compound diminished Aβ42 toxicity in the current AD Drosophila model by rescuing the rough eye phenotype, prolonging the lifespan and enhancing motor functions. Through Next-generation RNA-sequencing, immune response pathways were downregulated in response to THICAPA treatment. Thus, this study suggests THICAPA as a possible disease-modifying treatment for AD. |
| Wu, T., Deger, J. M., Ye, H., Guo, C., Dhindsa, J., Pekarek, B. T., Al-Ouran, R., Liu, Z., Al-Ramahi, I., Botas, J. and Shulman, J. M. (2023). Tau polarizes an aging transcriptional signature to excitatory neurons and glia. Elife 12. PubMed ID: 37219079
Summary: Aging is a major risk factor for Alzheimer's disease (AD), and cell-type vulnerability underlies its characteristic clinical manifestations. Longitudinal, single-cell RNA-sequencing was performed in Drosophila with pan-neuronal expression of human tau, which forms AD neurofibrillary tangle pathology. Whereas tau- and aging-induced gene expression strongly overlap (93%), they differ in the affected cell types. In contrast to the broad impact of aging, tau-triggered changes are strongly polarized to excitatory neurons and glia. Further, tau can either activate or suppress innate immune gene expression signatures in a cell-type-specific manner. Integration of cellular abundance and gene expression pinpoints nuclear factor kappa B signaling in neurons as a marker for cellular vulnerability. This study also highlights the conservation of cell-type-specific transcriptional patterns between Drosophila and human postmortem brain tissue. Overall, these results create a resource for dissection of dynamic, age-dependent gene expression changes at cellular resolution in a genetically tractable model of tauopathy. | Suzuki, M., Kuromi, H., Shindo, M., Sakata, N., Niimi, N., Fukui, K., Saitoe, M. and Sango, K. (2023). A Drosophila model of diabetic neuropathy reveals a role of proteasome activity in the glia. iScience 26(6): 106997. PubMed ID: 37378316
Summary: Diabetic peripheral neuropathy (DPN) is the most common chronic, progressive complication of diabetes mellitus. The main symptom is sensory loss; the molecular mechanisms are not fully understood. This study found that Drosophila fed a high-sugar diet, which induces diabetes-like phenotypes, exhibit impairment of noxious heat avoidance. The impairment of heat avoidance was associated with shrinkage of the leg neurons expressing the Drosophila transient receptor potential channel Painless. Using a candidate genetic screening approach proteasome modulator 9b (CG9588)/ was identified as one of the modulators of impairment of heat avoidance. It waS further showN that proteasome inhibition in the glia reversed the impairment of noxious heat avoidance, and heat-shock proteins and endolysosomal trafficking in the glia mediated the effect of proteasome inhibition. These results establish Drosophila as a useful system for exploring molecular mechanisms of diet-induced peripheral neuropathy and propose that the glial proteasome is one of the candidate therapeutic targets for DPN. |
Wednesday, January 3rd- Synapse, ER, and Vesicles |
| Miao, H., Millage, M., Rollins, K. R. and Blankenship, J. T. (2023). A Rab39-Klp98A-Rab35 endocytic recycling pathway is essential for rapid Golgi-dependent furrow ingression. Development 150(16). PubMed ID: 37590130
Summary: Ingression of the plasma membrane is an essential part of the cell topology-distorting repertoire and a key element in animal cell cytokinesis. Many embryos have rapid cleavage stages in which they are furrowing powerhouses, quickly forming and disassembling cleavage furrows on timescales of just minutes. Previous work has shown that cytoskeletal proteins and membrane trafficking coordinate to drive furrow Ingression, but where these membrane stores are derived from and how they are directed to furrowing processes has been less clear. This study identified an extensive Rab35/Rab4>Rab39/Klp98A>gt;trans-Golgi network (TGN) endocytic recycling pathway necessary for fast furrow ingression in the Drosophila embryo. Rab39 is present in vesiculotubular compartments at the TGN where it receives endocytically derived cargo through a Rab35/Rab4-dependent pathway. A Kinesin-3 family member, Klp98A, drives the movements and tubulation activities of Rab39, and disruption of this Rab39-Klp98A-Rab35 pathway causes deep furrow ingression defects and genomic instability. These data suggest that an endocytic recycling pathway rapidly remobilizes membrane cargo from the cell surface and directs it to the trans-Golgi network to permit the initiation of new cycles of cleavage furrow formation. | Maruzs, T., Feil-Borcsok, D., Lakatos, E., Juhasz, G., Blastyak, A., Hargitai, D., Jean, S., Lorincz, P. and Juhasz, G. (2023). Interaction of the sorting nexin 25 homologue Snazarus with Rab11 balances endocytic and secretory transport and maintains the ultrafiltration diaphragm in nephrocytes. Mol Biol Cell 34(9): ar87. PubMed ID: 37314856
Summary: Proper balance of exocytosis and endocytosis is important for the maintenance of plasma membrane lipid and protein homeostasis. This is especially critical in human podocytes and the podocyte-like Drosophila nephrocytes that both use a delicate diaphragm system with evolutionarily conserved components for ultrafiltration. This study shows that the sorting nexin 25 homologue Snazarus (Snz) binds to Rab11 and localizes to Rab11-positive recycling endosomes in Drosophila nephrocytes, unlike in fat cells where it is present in plasma membrane/lipid droplet/endoplasmic reticulum contact sites. loss of Snz leads to redistribution of Rab11 vesicles from the cell periphery and increases endocytic activity in nephrocytes. These changes are accompanied by defects in diaphragm protein distribution that resemble those seen in Rab11 gain-of-function cells. Of note, co-overexpression of Snz rescues diaphragm defects in Rab11 overexpressing cells, whereas snz knockdown in Rab11 overexpressing nephrocytes or simultaneous knockdown of snz and tbc1d8b encoding a Rab11 GTPase-activating protein (GAP) leads to massive expansion of the lacunar system that contains mislocalized diaphragm components: Sns and Pyd/ZO-1. Loss of Snz enhances while its overexpression impairs secretion, which, together with genetic epistasis analyses, suggest that Snz counteracts Rab11 to maintain the diaphragm via setting the proper balance of exocytosis and endocytosis. |
| Maddison, D. C., Malik, B., Amadio, L., Bis-Brewer, D. M., Zuchner, S., Peters, O. M. and Smith, G. A. (2023). COPI-regulated mitochondria-ER contact site formation maintains axonal integrity. Cell Rep 42(8): 112883. PubMed ID: 37498742
Summary: Coat protein complex I (COPI) is best known for its role in Golgi-endoplasmic reticulum (ER) trafficking, responsible for the retrograde transport of ER-resident proteins. The ER is crucial to neuronal function, regulating Ca(2+) homeostasis and the distribution and function of other organelles such as endosomes, peroxisomes, and mitochondria via functional contact sites. This study demonstrates that disruption of COPI results in mitochondrial dysfunction in Drosophila axons and human cells. The ER network is also disrupted, and the neurons undergo rapid degeneration. Mitochondria-ER contact sites (MERCS) are decreased in COPI-deficient axons, leading to Ca(2+) dysregulation, heightened mitophagy, and a decrease in respiratory capacity. Reintroducing MERCS is sufficient to rescue not only mitochondrial distribution and Ca(2+) uptake but also ER morphology, dramatically delaying neurodegeneration. This work demonstrates an important role for COPI-mediated trafficking in MERC formation, which is an essential process for maintaining axonal integrity. | Mohylyak, I., Bengochea, M., Pascual-Caro, C., Asfogo, N., Fonseca-Topp, S., Danda, N., Atak, Z. K., De Waegeneer, M., Placais, P. Y., Preat, T., Aerts, S., Corti, O., de Juan-Sanz, J. and Hassan, B. A. (2023). Developmental transcriptional control of mitochondrial homeostasis is required for activity-dependent synaptic connectivity. bioRxiv. PubMed ID: 37333418
Summary: During neuronal circuit formation, local control of axonal organelles ensures proper synaptic connectivity. Whether this process is genetically encoded is unclear and if so, its developmental regulatory mechanisms remain to be identified. It was hypothesized that developmental transcription factors regulate critical parameters of organelle homeostasis that contribute to circuit wiring. This study combined cell type-specific transcriptomics with a genetic screen to discover such factors. Telomeric Zinc finger-Associated Protein (TZAP; CG7101) as a temporal developmental regulator of neuronal mitochondrial homeostasis genes, including Pink1. In Drosophila, loss of dTzap function during visual circuit development leads to loss of activity-dependent synaptic connectivity, that can be rescued by Pink1 expression. At the cellular level, loss of dTzap/TZAP leads to defects in mitochondrial morphology, attenuated calcium uptake and reduced synaptic vesicle release in fly and mammalian neurons. These findings highlight developmental transcriptional regulation of mitochondrial homeostasis as a key factor in activity-dependent synaptic connectivity. |
| Rozenfeld, E., Ehmann, N., Manoim, J. E., Kittel, R. J. and Parnas, M. (2023). Homeostatic synaptic plasticity rescues neural coding reliability. Nat Commun 14(1): 2993. PubMed ID: 37225688
Summary: To survive, animals must recognize reoccurring stimuli. This necessitates a reliable stimulus representation by the neural code. While synaptic transmission underlies the propagation of neural codes, it is unclear how synaptic plasticity can maintain coding reliability. By studying the olfactory system of Drosophila melanogaster, this study aimed to obtain a deeper mechanistic understanding of how synaptic function shapes neural coding in the live, behaving animal. It was shown that the properties of the active zone (AZ), the presynaptic site of neurotransmitter release, are critical for generating a reliable neural code. Reducing neurotransmitter release probability of olfactory sensory neurons disrupts both neural coding and behavioral reliability. Strikingly, a target-specific homeostatic increase of AZ numbers rescues these defects within a day. These findings demonstrate an important role for synaptic plasticity in maintaining neural coding reliability and are of pathophysiological interest by uncovering an elegant mechanism through which the neural circuitry can counterbalance perturbations. . | Wang, R., Fortier, T. M., Chai, F., Miao, G., Shen, J. L., Restrepo, L. J., DiGiacomo, J. J., Velentzas, P. D. and Baehrecke, E. H. (2023). PINK1, Keap1, and Rtnl1 regulate selective clearance of endoplasmic reticulum during development. Cell. PubMed ID: 37633267
Summary: Selective clearance of organelles, including endoplasmic reticulum (ER) and mitochondria, by autophagy plays an important role in cell health. This study describes a developmentally programmed selective ER clearance by autophagy. This study shows that Parkinson's disease-associated PINK1, as well as Atl, Rtnl1, and Trp1 receptors, regulate ER clearance by autophagy. The E3 ubiquitin ligase Parkin functions downstream of PINK1 and is required for mitochondrial clearance while having the opposite function in ER clearance. By contrast, Keap1 and the E3 ubiquitin ligase Cullin3 function downstream of PINK1 to regulate ER clearance by influencing Rtnl1 and Atl. PINK1 regulates a change in Keap1 localization and Keap1-dependent ubiquitylation of the ER-phagy receptor Rtnl1 to facilitate ER clearance. Thus, PINK1 regulates the selective clearance of ER and mitochondria by influencing the balance of Keap1- and Parkin-dependent ubiquitylation of substrates that determine which organelle is removed by autophagy |
Tuesday, January 2nd - Signal Transduction |
| Sokolowski, D. J., Vasquez, O. E., Wilson, M. D., Sokolowski, M. B. and Anreiter, I. (2023). Transcriptomic effects of the foraging gene shed light on pathways of pleiotropy and plasticity. Ann N Y Acad Sci 1526(1): 99-113. PubMed ID: 37350250
Summary: >Genes are often pleiotropic and plastic in their expression, features which increase and diversify the functionality of the genome. The foraging (for) gene in Drosophila melanogaster is highly pleiotropic and a long-standing model for studying individual differences in behavior and plasticity from ethological, evolutionary, and genetic perspectives. Its pleiotropy is known to be linked to its complex molecular structure; however, the downstream pathways and interactors remain mostly elusive. To uncover these pathways and interactors and gain a better understanding of how pleiotropy and plasticity are achieved at the molecular level, this study explored the effects of different for alleles on gene expression at baseline and in response to 4 h of food deprivation, using RNA sequencing analysis in different Drosophila larval tissues. The results show tissue-specific transcriptomic dynamics influenced by for allelic variation and food deprivation, as well as genotype by treatment interactions. Differentially expressed genes yielded pathways linked to previously described for phenotypes and several potentially novel phenotypes. Together, these findings provide putative genes and pathways through which for might regulate its varied phenotypes in a pleiotropic, plastic, and gene-structure-dependent manner. | Shieh, B. H., Sun, W. and Ferng, D. (2023). A conventional PKC critical for both the light-dependent and the light-independent regulation of the actin cytoskeleton in Drosophila photoreceptors. J Biol Chem 299(6): 104822. PubMed ID: 37201584
Summary: Pkc53E is the second conventional protein kinase C (PKC) gene expressed in Drosophila photoreceptors; it encodes at least six transcripts generating four distinct protein isoforms including Pkc53E-B whose mRNA is preferentially expressed in photoreceptors. By characterizing transgenic lines expressing Pkc53E-B-GFP, this study showed Pkc53E-B is localized in the cytosol and rhabdomeres of photoreceptors, and the rhabdomeric localization appears dependent on the diurnal rhythm. A loss of function of pkc53E-B leads to light-dependent retinal degeneration. Interestingly, the knockdown of pkc53E also impacted the actin cytoskeleton of rhabdomeres in a light-independent manner. Here the Actin-GFP reporter is mislocalized and accumulated at the base of the rhabdomere, suggesting that Pkc53E regulates depolymerization of the actin microfilament. The light-dependent regulation of Pkc53E was demonstrated and it was demonstrated that activation of Pkc53 E can be independent of the phospholipase C PLCβ4/NorpA as degeneration of norpA(P24) photoreceptors was enhanced by a reduced Pkc53E activity. It was further shown that the activation of Pkc53E may involve the activation of Plc21C by Gqα. Taken together, Pkc53E-B appears to exert both constitutive and light-regulated activity to promote the maintenance of photoreceptors possibly by regulating the actin cytoskeleton. |
| Roberto, G. M., Boutet, A., Keil, S. and Emery, G. (2023). Dual regulation of Misshapen by Tao and Rap2l promotes collective cell migration. bioRxiv. PubMed ID: 37503122
Summary: Collective cell migration occurs in various biological processes such as development, wound healing and metastasis. During Drosophila oogenesis, border cells (BC) form a cluster that migrates collectively inside the egg chamber. The Ste20-like kinase Misshapen (Msn) is a key regulator of BC migration coordinating the restriction of protrusion formation and contractile forces within the cluster. This study demonstrates that the kinase Tao acts as an upstream activator of Msn in BCs. Depletion of Tao significantly impedes BC migration and produces a phenotype similar to Msn loss-of-function. Furthermore, it was shown that the localization of Msn relies on its CNH domain, which interacts with the small GTPase Rap2l. These findings indicate that Rap2l promotes the trafficking of Msn to the endolysosomal pathway. When Rap2l is depleted, the levels of Msn increase in the cytoplasm and at cell-cell junctions between BCs. Overall, these data suggest that Rap2l ensures that the levels of Msn are higher at the periphery of the cluster through the targeting of Msn to the degradative pathway. Together, this study identified two distinct regulatory mechanisms that ensure the appropriate distribution and activation of Msn in BCs. | Townson, J. M., Gomez-Lamarca, M. J., Santa Cruz Mateos, C. and Bray, S. J. (2023). OptIC-Notch reveals mechanism that regulates receptor interactions with CSL. Development 150(11). PubMed ID: 37294169
Summary: Active Notch signalling is elicited through receptor-ligand interactions that result in release of the Notch intracellular domain (NICD), which translocates into the nucleus. NICD activates transcription at target genes, forming a complex with the DNA-binding transcription factor CSL [CBF1/Su(H)/LAG-1] and co-activator Mastermind. However, CSL lacks its own nuclear localisation sequence, and it remains unclear where the tripartite complex is formed. To probe the mechanisms involved, an optogenetic approach was designed to control NICD release (OptIC-Notch) and monitored the subsequent complex formation and target gene activation. Strikingly, it was observed that, when uncleaved, OptIC-Notch sequestered CSL in the cytoplasm. Hypothesising that exposure of a juxta membrane φWφP motif is key to sequestration, this motif was masked with a second light-sensitive domain (OptIC-Notch{ω}), which was sufficient to prevent CSL sequestration. Furthermore, NICD produced by light-induced cleavage of OptIC-Notch or OptIC-Notch{ω} chaperoned CSL into the nucleus and induced target gene expression, showing efficient light-controlled activation. These results demonstrate that exposure of the φWφP motif leads to CSL recruitment and suggest this can occur in the cytoplasm prior to nuclear entry. |
| Prakash, A., Monteith, K. M., Bonnet, M. and Vale, P. F. (2023). Duox and Jak/Stat signalling influence disease tolerance in Drosophila during Pseudomonas entomophila infection. Dev Comp Immunol 147: 104756. PubMed ID: 37302730
Summary: Disease tolerance describes an infected host's ability to maintain health independently of the ability to clear microbe loads. The Jak/Stat pathway plays a pivotal role in humoral innate immunity by detecting tissue damage and triggering cellular renewal, making it a candidate tolerance mechanism. This study found that in Drosophila melanogaster infected with Pseudomonas entomophila disrupting ROS-producing dual oxidase (duox) or the negative regulator of Jak/Stat Socs36E, render male flies less tolerant. Another negative regulator of Jak/Stat, G9a - which has previously been associated with variable tolerance of viral infections - did not affect the rate of mortality with increasing microbe loads compared to flies with functional G9a, suggesting it does not affect tolerance of bacterial infection as in viral infection. These findings highlight that ROS production and Jak/Stat signalling influence the ability of flies to tolerate bacterial infection sex-specifically and may therefore contribute to sexually dimorphic infection outcomes in Drosophila. | Pierini, G. and Dahmann, C. (2023). Hedgehog morphogen gradient is robust towards variations in tissue morphology in Drosophila. Sci Rep 13(1): 8454. PubMed ID: 37231029
Summary: During tissue development, gradients of secreted signaling molecules known as morphogens provide cells with positional information. The mechanisms underlying morphogen spreading have been widely studied, however, it remains largely unexplored whether the shape of morphogen gradients is influenced by tissue morphology. This study developed an analysis pipeline to quantify the distribution of proteins within a curved tissue. This analyses was applied to the Hedgehog morphogen gradient in the Drosophila wing and eye-antennal imaginal discs, which are flat and curved tissues, respectively. Despite a different expression profile, the slope of the Hedgehog gradient was comparable between the two tissues. Moreover, inducing ectopic folds in wing imaginal discs did not affect the slope of the Hedgehog gradient. Suppressing curvature in the eye-antennal imaginal disc also did not alter the Hedgehog gradient slope but led to ectopic Hedgehog expression. In conclusion, through the development of an analysis pipeline that allows quantifying protein distribution in curved tissues, this study showed that the Hedgehog gradient is robust towards variations in tissue morphology. |
The Interactive Fly resides on the Society for Developmental Biology's Web server.