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August 2026 July 2026 June 2026 May 2026 April 2026 March 2026 February 2026 January 2026 December 2025 November 2025 October 2025 September 2025 August2025 July 2025 June2025 May 2025 April 2025 March 2025 February 2025 January 2025 December 2024 November 2024 October 2024 September 2024 August 2024 July 2024 June 2024 December 2023 December 2022 December 2021 December 2020 December 2019 | Koch, R., Nagoshi, E. (2025). Examining the potential involvement of NONO in TDP-43 proteinopathy in Drosophila. Eur J Neurosci, 61(1):e16632 PubMed ID: 39690447
Summary: The misfolding and aggregation of TAR DNA binding protein-43 (TDP-43), leading to the formation of cytoplasmic inclusions, emerge as a key pathological feature in a spectrum of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD), two ends of the same clinical, genetic, and pathological disease spectrum. TDP-43 shuttles between the nucleus and cytoplasm but forms nuclear bodies (NBs) in response to stress. These NBs partially colocalise with nuclear speckles and paraspeckles that sequester RNAs and proteins, thereby regulating many cellular functions. The laboratory of Steven Brown has recently found that the non-POU domain-containing octamer-binding protein (NONO), a component of paraspeckles, forms novel nuclear speckle-like structures in mouse cortical neurons in response to stress and sleep deprivation. These findings suggest the possibility of a functional link between NONO and TDP-43, potentially contributing to TDP-43 proteinopathy. This study demonstrate that pathological phenotypes caused by TDP-43 gain of function-locomotor defects and life span shortening-are exacerbated by silencing the Drosophila homolog of NONO, no on or off transient A (NonA), encoding a nuclear RNA-binding protein that regulates vision, courtship song production, circadian rhythms, and locomotor activity. Additionally, NonA silencing results in an increase in nuclear TDP-43 NBs. These results provide supporting evidence for the functional link between NONO and TDP-43 and lay the foundation for dissecting underlying mechanisms. | Gill, S., Mandigo, T. R., Elmali, A. D., Leger, B. S., Yang, B., Tran, S., Laosuntisuk, K., Lane, J. M., Bannister, D., Aonbangkhen, C., Ormerod, K. G., Mahama, B., Schuch, K. N., Elya, C., Akhund-Zade, J., Math, S. R., LoRocco, N. C., Seo, S., Maher, M., Kanca, O., Bebek, N., Karadeniz, D., Senel, G. B., Courage, C., Lehesjoki, A. E., Winkelman, J. W., Bellen, H. J., de Bivort, B., Hart, A. C., Littleton, J. T., Baykan, B., Doherty, C. J., Melkani, G. C., Prober, D. A., Woo, C. M., Saxena, R., Schreiber, S. L., Walker, J. A. (2024). A conserved role for ALG10/ALG10B and the N -glycosylation pathway in the sleep-epilepsy axis. medRxiv, PubMed ID: 39711723
Summary: Congenital disorders of glycosylation (CDG) comprise a class of inborn errors of metabolism resulting from pathogenic variants in genes coding for enzymes involved in the asparagine-linked glycosylation of proteins. Unexpectedly to date, no CDG has been described for ALG10, encoding the alpha-1,2-glucosyltransferase catalyzing the final step of lipid-linked oligosaccharide biosynthesis. Genome-wide association studies (GWAS) of human traits in the UK Biobank revealed significant SNP associations with short sleep duration, reduced napping frequency, later sleep timing and evening diurnal preference as well as cardiac traits at a genomic locus containing a pair of paralogous enzymes ALG10 and ALG10B. Modeling Alg10 loss in Drosophila, this study identified an essential role for the N -glycosylation pathway in maintaining appropriate neuronal firing activity, healthy sleep, preventing seizures, and cardiovascular homeostasis. This study further confirmed the broader relevance of neurological findings associated with Alg10 from humans and flies using zebrafish and nematodes and demonstrate conserved biochemical roles for N -glycosylation in Arabidopsis. A human subject is reported that was homozygous for variants in both ALG10 and ALG10B arising from a consanguineous marriage, with epilepsy, brain atrophy, and sleep abnormalities as predicted by the fly phenotype. Quantitative glycoproteomic analysis in the Drosophila model identifies potential key molecular targets for neurological symptoms of CDGs. |
| Mele, S., Martelli, F., Barlow, C. K., Jefferies, G., Dworkin, S., Christodoulou, J., Schittenhelm, R. B., Piper, M. D. W., Johnson, T. K. (2025). Valine Restriction Extends Survival in a Drosophila Model of Short-Chain Enoyl-CoA Hydratase 1 (ECHS1) Deficiency. J Inherit Metab Dis, 48(1):e12840 PubMed ID: 39727068
Summary: Short-chain enoyl-CoA hydratase 1 deficiency (ECHS1D) is a rare genetic disorder caused by biallelic pathogenic variants in the ECHS1 gene. ECHS1D is characterised by severe neurological and physical impairment that often leads to childhood mortality. Therapies such as protein and single nutrient-restricted diets show poor efficacy, whereas the development of new treatments is hindered by the low prevalence of the disorder and a lack of model systems for treatment testing. This study reports on the establishment of a Drosophila model of ECHS1D. Flies carrying mutations in Echs1 (CG6543) were characterised for their physical and metabolic phenotypes, and dietary intervention to improve fly model health was explored. The Echs1 null larvae recapitulated human ECHS1D phenotypes including poor motor behaviour and early mortality and could be rescued by the expression of a human ECHS1 transgene. Both restriction of valine in isolation, or all branched-chain amino acids (BCAAs-leucine, isoleucine and valine) together, extended larval survival, supporting the idea that reducing BCAA pathway catabolic flux is beneficial in this disorder. Further, metabolic profiling revealed substantial changes to carbohydrate metabolism, suggesting that Echs1 loss causes widespread metabolic dysregulation beyond valine metabolism. The similarities between Drosophila and human ECHS1D suggest that the fly model is a valuable animal system in which to explore mechanisms of pathogenesis and novel treatment options for this disorder. | Mishra, L., Mishra, M. (2024). Ribose-induced advanced glycation end products reduce the lifespan in Drosophila melanogaster by changing the redox state and down-regulating the Sirtuin genes. Biogerontology, 26(1):28 PubMed ID: 39702854
Summary: Advanced Glycation End (AGE) products are one such factor that accumulates during aging and age-related diseases. However, how exogenous AGE compounds cause aging is an area that needs to be explored. Specifically, how an organ undergoes aging and aging-related phenomena that need further investigation. The intestine is the most exposed area to food substances. How AGEs affect the intestine in terms of aging need to be explored. Drosophila melanogaster, a well-known model organism, is used to decode aging and age-associated phenomena. In this study, Ribose induced Advanced Glycation End products (Rib-AGE) fed to D. melanogaster was used to study the aging mechanism. The Rib-AGE-induced aging was checked in Drosophila. A series of changes was found in Rib-AGE-fed flies. Reactive oxygen species (ROS) and nitric oxide species (NOs) were higher in the Rib-AGE-fed flies, and the antioxidant level was lower. The intestinal permeability was altered. The microorganism load was higher inside the gut. The structural arrangement of the gut's microfilament was found to be damaged, and the nuclear shape was found to be irregular. Cell death within the gut was elevated in comparison to control. The food intake was found to be reduced. The relative mRNA expression of the histone deacetylases Sirtuin 2 and Sirtuin 6 gene of D. melanogaster was downregulated in Rib-AGE-fed flies compared to the control. All these findings strongly suggest that Rib-AGE accelerates aging and age-related disorders in D. melanogaster. |
| Bolshakova, O. I., Slobodina, A. D., Slepneva, E. E., Sarantseva, S. V. (2024). Acetyl-L-Carnitine Aids in Preservation of Cholinergic Neurons and Memory in the Drosophila melanogaster Model of Alzheimer's Disease. Curr Alzheimer Res, 21(8):557-565 PubMed ID: 39716786
Summary: The lack of effective therapy for the treatment of Alzheimer's disease demands both the search for new drugs and the reconsideration of already known substances currently used in other areas of medicine. Drosophila melanogaster offers the potential to model features of Alzheimer's disease, study disease mechanisms, and conduct drug screening. The purpose of this work was to analyze the neuroprotective properties of the drug "carnicetine", which is an acetylated form of the natural low molecular weight compound L-carnitine. The drug is able to cross the blood-brain barrier and is currently used as a means of improving cellular metabolism. Using tissue-specific drivers, direct expression of amyloid beta peptide (42 amino acids) was exhibited in certain groups of neurons in the Drosophila melanogaster brain, namely in dopaminergic and cholinergic neurons. The effect of acetyl-L-carnitine (carnicetine) on the death of these neurons and the memory of flies was analyzed. The expression of amyloid beta peptide in dopaminergic or cholinergic neurons resulted in neurodegeneration of cholinergic neurons in the Drosophila brain and memory impairment. The use of carnicetine added to animal food made it possible to treat these disorders. At the same time, no effect on dopaminergic neurons was noted. The data obtained confirmed the neuroprotective properties of the drug under study, demonstrating its participation in the restoration of the cholinergic system and the feasibility of using carnicetine for the treatment of Alzheimer's disease. | Gonskikh, Y., Tirrito, C., Bommisetti, P., Mendoza-Figueroa, M. S., Stoute, J., Kim, J., Wang, Q., Song, Y., Liu, K. F. (2025). Spatial regulation of NSUN2-mediated tRNA m5C installation in cognitive function. Nucleic Acids Res, 53(2) PubMed ID: 39673800
Summary: Enzyme-mediated modifications of tRNA, such as 5-methylcytosine (m5C) installed by nuclear-enriched NOP2/Sun RNA methyltransferase 2 (NSUN2), play a critical role in neuronal development and function. However, understanding of these modifications' spatial installation and biological functions remains incomplete. This study demonstrates that a nucleoplasm-localized G679R NSUN2 mutant, linked to intellectual disability, diminishes NSUN2-mediated tRNA m5C in human cell lines and Drosophila. These findings indicate that inability of RNA methyltransferase G679R-NSUN2 to install m5C is primarily attributed to its reduced binding to tRNA rather than its nucleoplasmic localization. Conversely, an NSUN2 variant lacking an internal intrinsically disordered region (ΔIDR-NSUN2) can install ~80% m5C within the nucleoplasm. Furthermore, this study showed that tRNA m5C levels are positively correlated to cognitive performance in Drosophila, where expressing G679R-NSUN2 leads to the most severe social behavioral deficits while expressing ΔIDR-NSUN2 results in less pronounced deficits. This work illuminates the molecular mechanism underlying G679R disease mutation in cognitive function and offers valuable insights into the significance of the cellular localization of m5C installation on tRNA for neuronal function. |
Thursday, October 1st - Stress |
| Vrdoljak, J., Soto, I. M., Carreira, V. P., Padro, J. (2025). Environmental stress differentially affects phenotypic modularity and fluctuating asymmetry in generalist and specialist cactophilic Drosophila. Journal of evolutionary biology, 38(3):404-416 PubMed ID: 39821346
Summary: Modularity and developmental (in)stability have the potential to influence phenotype production and, consequently, the evolutionary trajectories of species. Depending on the environmental stress factors involved and the buffering capacity of an organism, different developmental outcomes are expected. Cactophilic Drosophila species provide an established eco-evolutionary model with well-studied ecological conditions, making them ideal for studying these phenomena. This study investigated how variations in larval diet and exposure to alkaloids on primary and secondary host plants affect the degree of integration/modularity and fluctuating asymmetry (FA, a proxy for developmental instability) of wing shape in two sibling species with different degrees of specialisation: Drosophila buzzatii (generalist) and Drosophila koepferae (specialist). Additionally, the anterior-posterior modular configuration was compared with a recently proposed proximal-distal modular configuration. The results revealed greater independence among proximal-distal modules compared to anterior-posterior modules. Moreover, sex-specific responses were observed, with males exhibiting greater susceptibility to stressful environments than females. Each species showed a particular trait pattern across treatments: D. buzzatii showed increased integration and FA when reared in a nutrient-poor, alkaloid-rich secondary host, while D. koepferae displayed similar responses in novel environments characterised by double doses of alkaloids on the secondary host plant. These findings align with the generalist-specialist paradigm, suggesting that specialists may be challenged by novel environments, whereas generalists may be more affected by stressful conditions. This study highlights the importance of considering each part of the proximal-distal wing axis independently, and the need to consider ecological-evolutionary history when investigating the relationship between complex phenotypic traits and environmental stress. | Shields, S., Gregory, E., Wilkes, O., Gozes, I., Sanchez-Soriano, N. (2025). Oxidative Stress Promotes Axonal Atrophy through Alterations in Microtubules and EB1 Function. Aging Dis, PubMed ID: 39908272
Summary: Axons are crucial for transmitting neurochemical signals. As organisms age, the ability of neurons to maintain their axons declines; hence, aged axons are more susceptible to damage or dysfunction. Understanding how aging causes axonal vulnerability is crucial for developing strategies to enhance overall resilience of neurons and prevent neuronal deterioration during aging and in age-related neurodegenerative diseases. Increasing levels of reactive oxygen species (ROS) causes oxidative stress - a hallmark of aging and age-related diseases. Despite this association, a causal relationship between oxidative stress and neuronal aging remains unclear, particularly in how subcellular physiology may be affected by ROS. By using Drosophila-derived primary neuronal cultures and a recently developed in vivo neuronal model of aging, which involves the visualisation of Drosophila medulla neurons, this study investigated the interplay between oxidative stress, neuronal aging and the microtubule cytoskeleton. The results showed that oxidative stress is a key driver of axonal and synaptic decay, as shown by an enhanced appearance of axonal swellings, microtubule alterations (in both axons and synapses) and morphological transformation of axonal terminals during aging. Increasing the levels of ROS sensitises microtubule plus end-binding protein 1 (EB1), leading to microtubule defects that effect neuronal integrity. Furthermore, manipulating EB1 proved to be a valuable therapeutic strategy to prevent aging hallmarks enhanced in conditions of elevated ROS. In summary, a mechanistic pathway linking cellular oxidative stress with changes in the microtubule cytoskeleton leading to axonal deterioration during aging was demonstrated and evidence was provided of the therapeutic potential of enhancing microtubule plus-end physiology to improve the resilience of axons. |
| Hunter-Manseau, F., Cormier, J., Pichaud, N. (2025). From molecular to physiological responses: improved stress tolerance and longevity in Drosophila melanogaster under fluctuating thermal regimes. J Exp Biol, 228(2) PubMed ID: 39698946
Summary: Climate change introduces greater thermal variability, profoundly affecting ectothermic species whose body temperatures rely heavily on the environment. Understanding the physiological and metabolic responses to such variability is crucial for predicting how these species will cope with changing climates. This study investigates how chronic thermal stress impacts mitochondrial metabolism and physiological parameters in Drosophila melanogaster, hypothesizing that a fluctuating thermal regime (FTR) activates protective mechanisms enhancing stress tolerance and longevity. To test this, Drosophila were exposed to constant 24°C or to an FTR of 24°C:15°C (day:night) cycle following an initial 5 day period at 24°C. The FTR group exhibited rapid transcript level changes after the first day of FTR, particularly those related to heat shock proteins, mitophagy and regulatory factors, which returned to initial levels after 5 days. Mitochondrial respiration rates initially decreased after 1 and 2 days of FTR, then recovered by day 5, indicating rapid acclimation. Enhanced antioxidant enzyme activities were observed early in the FTR group, after 1 day for mtSOD and SODcyt+ext and 3 days for both SOD and catalase, followed by a decline by day 5, suggesting efficient oxidative stress management. The FTR group showed lower CTmax on day 3, reflecting possible physiological strain at that time point, and complete recovery by day 5. Longevity increased under FTR, highlighting the activation of protective mechanisms with beneficial long-term effects. These results suggest that FTR prompts a temporal succession of rapid physiological adjustments at different levels of organisation, enhancing long-term survival in D. melanogaster. | Dhadde, S. B., Kalshetti, M. S. (2025). Chromium-histidine complex enhances reproductive physiology and development in Drosophila melanogaster by modulating oxidative stress. Biometals, 38(1):321-335 PubMed ID: 39680280
Summary: The interaction of metal ions with biological systems plays a critical role in cellular functions, including oxidative stress regulation and metabolic health. This study aimed to explore the effects of the chromium-histidine complex [Cr(hist)(3)] on reproductive success, developmental processes, and oxidative stress defence in Drosophila melanogaster. Wild-type D. melanogaster flies were exposed to Cr(hist)(3) at concentrations of 5, 10, 15, and 20 μg/ml, and physiological parameters-including fecundity, fertility, developmental timelines, and antioxidant enzyme activity-were measured. The results indicate that Cr(hist)(3) at 15 μg/ml optimally enhanced reproductive health and developmental efficiency. Specifically, fecundity and fertility increased by 15.6% and 15.5%, respectively, and egg-to-adult viability improved by 15.6% compared to controls. Developmental timelines were shortened, with larval and pupal periods reduced by 7.6% and 7.1%. Additionally, Cr(hist)(3) treatment led to a significant downregulation of lipid peroxidation (MDA) by 17.54% and upregulation in antioxidant enzymes (catalase, glutathione-S-transferase, and superoxide dismutase), indicating improved cellular defence against oxidative damage. Flies treated with 15 μg/ml Cr(hist)(3)(3) also exhibited a 9.7% increase in lifespan. These findings suggest that Cr(hist)(3) enhances reproductive success and developmental dynamics through oxidative stress regulation, highlighting its potential for applications in insect health and stress management. This study contributes to the understanding of metal ion interactions in biological systems and their physiological effects. |
| Shekhar, S., Tracy, C., Lidsky, P. V., Andino, R., Wert, K. J., Kramer, H. (2025). Sensory quiescence induces a cell-non-autonomous integrated stress response curbed by condensate formation of the ATF4 and XRP1 effectors. Nature communications, 16(1):252 PubMed ID: 39747204
Summary: Sensory disabilities have been identified as significant risk factors for dementia but underlying molecular mechanisms are unknown. In different Drosophila models with loss of sensory input, this study observed non-autonomous induction of the integrated stress response (ISR) deep in the brain, as indicated by ATF4 and XRP1. Unlike during canonical ISR, however, the ATF4 and XRP1 transcription factors are enriched in cytosolic granules that are positive for RNA and the stress granule markers Caprin, FMR1, and p62, and are reversible upon restoration of vision for blind flies. Cytosolic restraint of the ATF4 and XRP1 transcription factors dampens expression of their downstream targets including genes of cell death pathways activated during chronic cellular stress and thus constitutes a chronic stress protective response (CSPR). Cytosolic granules containing both p62 and ATF4 are also evident in the thalamus and hippocampus of mouse models of congenital or degenerative blindness. These data indicate a conserved link between loss of sensory input and curbed stress responses critical for protein quality control in the brain. | Romano, N. C, Marchetti, M., Marangoni, A., Leo, L., Retrosi, D., Rosato, E., Fanti, L. (2024). Neuronal Progenitors Suffer Genotoxic Stress in the Drosophila Clock Mutant per(0). Cells, 13(23) PubMed ID: 39682693
Summary: The physiological role and the molecular architecture of the circadian clock in fully developed organisms are well established. Yet, there is limited understanding of the function of the clock during ontogenesis. This study used a null mutant (per0) of the clock gene period (per) in Drosophila melanogaster to ask whether PER may play a role during normal brain development. In third-instar larvae, per resulted in increased genotoxic stress compared to wild-type controls. Increased double-strand DNA breaks in the central nervous system and chromosome aberrations were detected in dividing neuronal precursor cells. Reactive oxygen species (ROS) are causal to the genotoxic effect, and expression of PER in glia is necessary and sufficient to suppress such a phenotype. Finally, the absence of PER may result in less condensed chromatin, which contributes to DNA damage. |
Wednesday September 30th - RNA Interference |
| Zhang, S., Wang, R., Luo, K., Gu, S., Liu, X., Wang, J., Zhang, L., Sun, L. (2025). Dynamics and regulatory roles of RNA m(6)A methylation in unbalanced genomes. eLife, 13 PubMed ID: 39853090
Summary: N(6)-methyladenosine (m(6)A) in eukaryotic RNA is an epigenetic modification that is critical for RNA metabolism, gene expression regulation, and the development of organisms. Aberrant expression of m(6)A components appears in a variety of human diseases. RNA m(6)A modification in Drosophila has proven to be involved in sex determination regulated by Sxl and may affect X chromosome expression through the MSL complex. The dosage-related effects under the condition of genomic imbalance (i.e. aneuploidy) are related to various epigenetic regulatory mechanisms. This study investigated the roles of RNA m(6)A modification in unbalanced genomes using aneuploid Drosophila. The results showed that the expression of m(6)A components changed significantly under genomic imbalance, and affected the abundance and genome-wide distribution of m(6)A, which may be related to the developmental abnormalities of aneuploids. The relationships between methylation status and classical dosage effect, dosage compensation, and inverse dosage effect were also studied. In addition, it was demonstrated that RNA m(6)A methylation may affect dosage-dependent gene regulation through dosage-sensitive modifiers, alternative splicing, the MSL complex, and other processes. More interestingly, there seems to be a close relationship between MSL complex and RNA m(6)A modification. It was found that ectopically overexpressed MSL complex, especially the levels of H4K16Ac through MOF, could influence the expression levels of m(6)A modification and genomic imbalance may be involved in this interaction. This study found that m(6)A could affect the levels of H4K16Ac through MOF, a component of the MSL complex, and that genomic imbalance may be involved in this interaction. Altogether, this work reveals the dynamic and regulatory role of RNA m(6)A modification in unbalanced genomes, and may shed new light on the mechanisms of aneuploidy-related developmental abnormalities and diseases. | Kochendorfer, W., Forstemann, K. (2026). Induced RNA Interference Can Suppress Persistent Drosophila A Virus (DAV) Infection in Cultured Drosophila Melanogaster S2 Cells. Noncoding RNA, 12(4) PubMed ID: 42646359
Summary: The RNA interference (RNAi) pathway is a highly conserved antiviral mechanism in eukaryotes, including insects such as fruit flies. Many viruses have therefore evolved mechanisms that protect their transcripts and/or genomes; how effectively RNAi can act is thus a question that must be answered case-by-case. This study demonstrates that the RNAi machinery can successfully combat Drosophila A virus (DAV) in persistently infected Drosophila melanogaster S2 cell lines, but only when supported with exogenous triggers. Since such an infection poses a challenge to the fitness of cells and the reproducibility of results obtained with them, the approach of this study provides a convenient method to recover precious experimentally modified cell lines from infection through the application of exogenous double-stranded RNA (dsRNA) targeting the DAV sequence. The in vitro transcribed dsRNAs were applied to infected S2 cells via direct "soaking," utilizing the cells' natural endocytic uptake. Treatment efficacy was monitored via RT-PCR-based detection of viral sequences, and the results demonstrate that continued application of DAV-specific dsRNAs led to a reduction in viral abundance and all eight tested cell lines appeared DAV-negative within several weeks of treatment. While a set of cell lines exhibited viral recurrence several weeks after the cessation of treatment, others remained virus-free for at least 16 weeks, suggesting that a permanent "cure" can indeed be achieved. Notably, while RNAi activation effectively cleared DAV in some cell lines, no beneficial effect was observed for a concomitantly applied Drosophila X-virus (DXV) treatment in the co-infected cultures. This suggests that DXV has more efficient evasion mechanisms but cannot protect DAV in trans. This protocol thus provides a robust, scalable approach for clearing persistent DAV infections, but may not be effective against all viruses known to infect Drosophila cell cultures. |
| Hiers, N. M., Li, L., Li, T., Sheng, P., Wang, Y., Traugot, C. M., Yao, M., Xie, M. (2024). An endogenous cluster of target-directed microRNA degradation sites induces decay of distinct microRNA families. bioRxiv, PubMed ID: 39713366
Summary: While much is known about miRNA biogenesis and canonical miRNA targeting, relatively less is understood about miRNA decay. The major miRNA decay pathway in metazoans is mediated through target-directed miRNA degradation (TDMD), in which certain RNAs can "trigger" miRNA decay. All known triggers for TDMD base pair with the miRNA seed, and extensively base pair on the miRNA 3' end, a pattern that supposedly induces a TDMD-competent conformational change of Argonaute (Ago), allowing for miRNA turnover. This study utilized Ago1-CLASH to find that the Drosophila transcript Kah contains at least two triggers, a "trigger cluster", against miR-9b and the miR-279 family. One of these triggers contains minimal/non-canonical 3' end base pairing but is still sufficient to induce TDMD of the entire miR-279 family. These clustered triggers likely lack cooperativity, the minimal 3' pairing is required for miR-279 family turnover, and the in-cell RNA structure of the Kah trigger clusters. Overall, this study expands the list of endogenous triggers and the unexpectedly complex regulatory network governing miRNA degradation (Hiers, 2024). | Chen, J., Liu, N., Qi, H., Neuenkirchen, N., Huang, Y., Lin, H. (2025). Piwi regulates the usage of alternative transcription start sites in the Drosophila ovary. Nucleic Acids Res, 53(1) PubMed ID: 39657757
Summary: Alternative transcription initiation, which refers to the transcription of a gene from different transcription start sites (TSSs), is prevalent across metazoans and has important biological functions. Although transcriptional regulation has been extensively studied, the mechanism that selects one TSS over others within a gene remains elusive. Using the Cap Analysis of Gene Expression sequencing (CAGE-seq) method, this study discovered that Piwi, an RNA-binding protein, regulates TSS usage in at least 87 genes. In piwi-deficient Drosophila ovaries, these genes displayed significantly altered TSS usage (ATU). The regulation of TSS usage occurred in both germline and somatic cells in ovaries, as well as in cultured ovarian somatic cells (OSCs). Correspondingly, RNA Polymerase II (Pol II) initiation and elongation at the TSSs of ATU genes were affected in germline-piwi-knockdown ovaries and piwi-knockdown OSCs. Furthermore, this study identified a Facilitates Chromatin Transcription (FACT) complex component, Ssrp, that is essential for mRNA elongation, as a novel interactor of Piwi in the nucleus. Temporally controlled knockdown of ssrp affected TSS usage in ATU genes, whereas overexpression of ssrp partially rescued the TSS usage of ATU genes in piwi mutant ovaries. Thus, Piwi may interact with Ssrp to regulate TSS usage in Drosophila ovaries by affecting Pol II initiation and elongation. |
| Chen, J., Bai, Y., Huang, Y., Cui, M., Wang, Y., Gu, Z., Wu, X., Li, Y., Rong, Y. S. (2024). The Ptch/SPOUT1 methyltransferase deposits an m(3)U modification on 28S rRNA for normal ribosomal function in flies and humans. Sci Adv, 10(50):eadr1743 PubMed ID: 39671501
Summary: The ribosomal RNA (rRNA) is one of the most heavily modified RNA species in nature. Although advanced knowledge of the sites is available, functions, and the enzymology of many of the rRNA modifications from all kingdoms of life, basic understanding is lacking of many of those that are not universally present. A single N(3) modified uridine base (m(3)U) was identified to be present on the 28S rRNA from humans and frogs but absent in bacteria or yeast. This study shows that the equivalent m(3)U is present in Drosophila and that the Ptch/CG12128 enzyme and its human homolog SPOUT1 are both necessary and sufficient for carrying out the modification. The Ptch-modified U is at a functional center of the large ribosomal subunit, and, consistently, ptch-mutant cells suffer loss of ribosomal functions. SPOUT1, suggested to be the most druggable RNA methyltransferases in humans, represents a unique target where ribosomal functions could be specifically compromised in cancer cells. | Bormann, A., Korner, M. B., Dahse, A. K., Glaser, M. S., Irmer, J., Lede, V., Alenfelder, J., Lehmann, J., Hall, D. C. N., Thane, M., Schleyer, M., Kostenis, E., Schoneberg, T., Bigl, M., Langenhan, T., Ljaschenko, D., Scholz, N. (2025). Intron retention of an adhesion GPCR generates 1TM isoforms required for 7TM-GPCR function. Cell Rep, 44(1):115078 PubMed ID: 39705141
Summary: Adhesion G protein-coupled receptors (aGPCRs) are expressed in all organs and are involved in various mechanobiological processes. They are heavily alternatively spliced, forecasting an extraordinary molecular structural diversity. This study uncovered the existence of unconventional single-transmembrane (1TM)-containing ADGRL/Cirl proteins devoid of the conventional GPCR layout (i.e., the 7TM signaling unit) in Drosophila. These 1TM proteins are made as a result of intron retention and provide an N-terminal fragment that acts as an interactor to allow Gαo-dependent signaling through conventional 7TM-containing Cirl isoforms encoded by the same gene. This molecular mechanism determines sensory precision of neurons in response to mechanical stimulation in vivo. This action mode of aGPCR provides a promising entry point for experimental and therapeutic approaches to intervene in aGPCR signaling and implicates alternative splicing as a physiological strategy to express a given aGPCR together with its molecular interactor. |
Tuesday September 29th - Gonads |
| Galletta, B. J., Konstantinidou, P., Haase, A. D., Rusan, N. M. (2025). A deficiency screen identifies genomic regions critical for sperm head-tail connection. G3 (Bethesda), 15(2) PubMed ID: 39700389
Summary: The Sperm Neck provides a stable connection between the sperm head and tail, which is critical for fertility in species with flagellated sperm. Within the Sperm Neck, the Head-Tail Coupling Apparatus serves as the critical link between the nucleus (head) and the axoneme (tail) via the centriole. To identify regions of the Drosophila melanogaster genome that contain genetic elements that influence Head-Tail Coupling Apparatus formation, a 2 part screen was undertaken using the Drosophila Deficiency kit. For this screen, a sensitized genetic background was utilized that overexpresses the pericentriolar material regulatory protein Pericentrin-Like Protein. Previous work has shown that Pericentrin-Like Protein overexpression disrupts the head-tail connection in some spermatids, but not to a degree sufficient to reduce fertility. In the first step of the screen, tests were performed for deficiencies that in combination with Pericentrin-Like Protein overexpression causes a reduction in fertility. Eleven regions of the genome were identified that resulted in an enhanced fertility defect when combined with Pericentrin-Like Protein overexpression. In the second step of the screen, these deficiencies were screened for their ability to enhance the head-tail connection defect caused by Pericentrin-Like Protein overexpression, finding 6 genomic regions. Smaller deficiencies were tested to narrow the region of the genome that contained these enhancers, and the expression patterns were examined of the genes within these deficiencies using publicly available datasets of Drosophila tissue RNAseq and Drosophila testes snRNAseq. In total, this analysis suggests that some deficiencies may contain single genes that influence Head-Tail Coupling Apparatus formation or fertility, while other deficiencies appear to be genomic regions rich in testis-expressed genes that might affect the Head-Tail Coupling Apparatus through complex, multigene interactions. | Riparbelli, M. G., Migliorini, M., Callaini, G. (2025). Astral Microtubules Are Dispensable for Pavarotti Localization During Drosophila Spermatogonial Mitoses. Cytoskeleton (Hoboken, NJ), PubMed ID: 39754387
Summary: This study examined dynamic of the kinesin-like Pavarotti (Pav) during male gametogenesis of wild-type and Sas-4 mutant flies. Pav localizes to the equatorial region and the inner central spindle of late anaphase wild-type spermatogonia and displays a strong concentration at the midbody during late telophase. At metaphase of the first meiotic division, Pav shows widespread localization on the equatorial region of the spermatocytes. This unusual distribution restricts and enhances during anaphase where antiparallel cortical microtubules overlap. Additional Pav staining is also found in the inner central spindle where the microtubules overlap between the segregating chromosomes. At late telophase, Pav accumulates to the midbody and on a weak ring that surround the cytoplasmic bridges. Pav localizes in an equatorial discontinuous ring of Sas4 spermatogonia where the non-centrosomal microtubules overlap, but the motor protein is absent in the interior central spindle where the inner microtubules are lacking. However, the anastral spindles properly support cell division, suggesting that astral microtubules are dispensable for Pav localization in the Sas4 spermatogonial cell cortex. This function is presumably replaced by the antiparallel cortical microtubules extending from the acentriolar polar regions. In contrast, the majority of the meiotic spindles in Sas4 mutant testes do not progress beyond late anaphase, and only a small fraction of the primary spermatocytes experienced an abnormal division with the assembly of aberrant telophase spindles. Pav accumulates around the chromatin clusters or enhanced at the plus ends of the antiparallel non-centrosomal cortical bundles of microtubules. However, these bundles are not arranged properly in the equatorial region of the cell and cytokinesis is abnormal or fails. Therefore, the observations in Sas4 mutant testes suggest that the spermatogonial mitoses correctly occur in the absence of astral microtubules, whereas meiotic divisions fail. |
| Mao, B., Wang, Y. Y., Li, S. Y., Fu, Y., Xiao, Y. L., Wang, Y. F. (2025). A potential role for the interaction of Wolbachia surface proteins with the Drosophila microtubulin in maintenance of endosymbiosis and affecting spermiogenesis. J Insect Physiol, 160:104743 PubMed ID: 39709001
Summary: Wolbachia, as a widely infected intracellular symbiotic bacterium in Arthropoda, is able to manipulate the reproduction of insect hosts for facilitating their own transmission. Cytoplasmic incompatibility (CI) is the most common phenotype that Wolbachia induced in insect hosts where they resulted in the failure of uninfected egg hatch when fertilized with the sperm derived from Wolbachia-infected males, suggesting that the sperm are modified by Wolbachia during spermatogenesis. Although the molecular mechanisms of CI are beginning to be understood, the effects of Wolbachia on the symbiotic relationship and the proper dynamics of spermatogenesis have not yet been fully investigated. This study report that Wolbachia infection induced a significant upregulation of betaTub85D in the testis of Drosophila melanogaster. Knockdown of betaTub85D in fly testes resulted in significant decrease in the copy number of Wolbachia surface protein gene (wsp), indicating a notable reduction of Wolbachia density. Pull-down analyses revealed that WSP interacted with the betaTub85D of D. melanogaster. Wolbachia infection altered the interactome between betaTub85D and other proteins in the testes, and may thus change the protein synthesis and metabolic pathways. Wolbachia infection induced not only an interaction of betaTub85D with Mst77F but also increase in phosphorylated Mst77F. These results suggest that Wolbachia WSP protein might play important roles in anchoring the endosymbiont to the host's cytoskeleton and consequently interfere the interactions among key proteins involved in spermatogenesis in the insect host testes, resulting in modified sperm. | Das, S., Hegde, S., Wagh, N., Sudhakaran, J., Roy, A. E., Deshpande, G., Ratnaparkhi, G. S. (2024). Caspar specifies primordial germ cell count and identity in Drosophila melanogaster. Elife, 13 PubMed ID: 39671304
Summary: Repurposing of pleiotropic factors during execution of diverse cellular processes has emerged as a regulatory paradigm. Embryonic development in metazoans is controlled by maternal factors deposited in the egg during oogenesis. This study explored maternal role(s) of Caspar (Casp), the Drosophila orthologue of human Fas-associated factor-1 (FAF1) originally implicated in host-defense as a negative regulator of NF-kappaB signaling. Maternal loss of either Casp or it's protein partner, transitional endoplasmic reticulum 94 (TER94) leads to partial embryonic lethality correlated with aberrant centrosome behavior, cytoskeletal abnormalities, and defective gastrulation. Although ubiquitously distributed, both proteins are enriched in the primordial germ cells (PGCs), and in keeping with the centrosome problems, mutant embryos display a significant reduction in the PGC count. Moreover, the total number of pole buds is directly proportional to the level of Casp. Consistently, it's 'loss' and 'gain' results in respective reduction and increase in the Oskar protein levels, the master determinant of PGC fate. To elucidate this regulatory loop, several known components of mid-blastula transition and the translational repressor Smaug, a zygotic regulator of germ cell specification, was identified as a potential critical target. A detailed structure-function analysis of Casp aimed at understanding its novel involvement during PGC development is presented. |
| Azlan, A., Zhu, L., Fukunaga, R. (2025). Female-germline specific protein Sakura interacts with Otu and is crucial for germline stem cell renewal and differentiation and oogenesis. bioRxiv, PubMed ID: 39651236
Summary: During oogenesis, self-renewal and differentiation of germline stem cells (GSCs) must be tightly regulated. The Drosophila female germline serves as an excellent model for studying these regulatory mechanisms. This study reports that a previously uncharacterized gene CG14545, which was named sakura (Flybase name: Bourbon), is essential for oogenesis and female fertility in Drosophila. Sakura is predominantly expressed in the ovaries, particularly in the germline cells, including GSCs. sakura null mutant female flies display rudimentary ovaries with germline-less and tumorous phenotypes, fail to produce eggs, and are completely sterile. The germline-specific depletion of sakura impairs Dpp/BMP signaling, leading to aberrant bag-of-marbles (bam) expression, resulting in faulty differentiation and loss of GSCs. sakura is also necessary for normal levels of piwi-interacting RNAs (piRNAs) levels and for female-specific splicing of sex-lethal (sxl), a master regulator of sex identity determination. Ovarian Tumor (Otu) was identified as a protein binding partner of Sakura, and loss of otu was found to phenocopy loss of sakura in ovaries. Thus, this study identified Sakura as a crucial factor for GSC renewal and differentiation and oogenesis, and it is proposed that Sakura and Otu function together in these processes. | Milano, S. N., Bayer, L. V., Ko, J. J., Casella, C. E., Bratu, D. P. (2025). The role of ER exit sites in maintaining P-body organization and integrity during Drosophila melanogaster oogenesis. EMBO Rep, 26(2):494-520 PubMed ID: 39653851
Summary: Processing bodies (P-bodies) are cytoplasmic membrane-less organelles which host multiple mRNA processing events. While the fundamental principles of P-body organization are beginning to be elucidated in vitro, a nuanced understanding of how their assembly is regulated in vivo remains elusive. This study investigated the potential link between ER exit sites and P-bodies in Drosophila melanogaster egg chambers. Employing a combination of live and super-resolution imaging, this study found that P-bodies associated with ER exit sites are larger and less mobile than cytoplasmic P-bodies, indicating that they constitute a distinct class of P-bodies. Moreover, it was demonstrated that altering the composition of ER exit sites has differential effects on core P-body proteins (Me31B, Cup, and Trailer Hitch), suggesting a potential role for ER exit sites in P-body organization. Furthermore, this study showed that in the absence of ER exit sites, P-body integrity is compromised and the stability and translational repression efficiency of the maternal mRNA, oskar, are reduced. Together, these data highlights the crucial role of ER exit sites in governing P-body organization. |
Monday September 28th - Chromatin |
| Chavan, A., Skrutl, L., Uliana, F., Pfister, M., Brandle, F., Tirian, L., Baptista, D., Handler, D., Burke, D., Sintsova, A., Beltrao, P., Brennecke, J., Jagannathan, M. (2025). Multi-tissue characterization of the constitutive heterochromatin proteome in Drosophila identifies a link between satellite DNA organization and transposon repression. PLoS biology, 23(1):e3002984 PubMed ID: 39813297
Summary: Noncoding satellite DNA repeats are abundant at the pericentromeric heterochromatin of eukaryotic chromosomes. During interphase, sequence-specific DNA-binding proteins cluster these repeats from multiple chromosomes into nuclear foci known as chromocenters. Despite the pivotal role of chromocenters in cellular processes like genome encapsulation and gene repression, the associated proteins remain incompletely characterized. This study used 2 satellite DNA-binding proteins, D1 and Prod, as baits to characterize the chromocenter-associated proteome in Drosophila embryos, ovaries, and testes through quantitative mass spectrometry. D1- and Prod-associated proteins were identified, including known heterochromatin proteins as well as proteins previously unlinked to satellite DNA or chromocenters, thereby laying the foundation for a comprehensive understanding of cellular functions enabled by satellite DNA repeats and their associated proteins. Interestingly, multiple components of the transposon-silencing piRNA pathway are associated with D1 and Prod in embryos. Using genetics, transcriptomics, and small RNA profiling, flies lacking D1 during embryogenesis were shown to exhibit transposon expression and gonadal atrophy as adults. It was further demonstrated that this gonadal atrophy can be rescued by mutating the checkpoint kinase, Chk2, which mediates germ cell arrest in response to transposon mobilization. Thus, this study revealed that a satellite DNA-binding protein functions during embryogenesis to silence transposons, in a manner that is heritable across later stages of development. | Pazhayam, N. M., Sagar, S., Sekelsky, J. (2024). Suppression of meiotic crossovers in pericentromeric heterochromatin requires synaptonemal complex and meiotic recombination factors in Drosophila melanogaster. bioRxiv, PubMed ID: 39763933
Summary: The centromere effect (CE) is a meiotic phenomenon that ensures meiotic crossover suppression in pericentromeric regions. Despite being a critical safeguard against nondisjunction, the mechanisms behind the CE remain unknown. Previous studies have shown that various regions of the Drosophila pericentromere, encompassing proximal euchromatin, beta and alpha heterochromatin, undergo varying levels of crossover suppression, raising the question of whether distinct mechanisms establish the CE in these different regions. To address this question, it was asked whether different pericentromeric regions respond differently to mutations that impair various features that may play a role in the CE. In flies with a mutation that affects the synaptonemal complex (SC), a structure is hypothesized to have important roles in recombination and crossover patterning, a significant redistribution of pericentromeric crossovers was observed from proximal euchromatin towards beta heterochromatin but not alpha heterochromatin, indicating a role for the SC in suppressing crossovers in beta heterochromatin. In flies mutant for mei-218 or rec, which encode components of a critical pro-crossover complex, there was a more extreme redistribution of pericentromeric crossovers towards both beta and alpha heterochromatin, suggesting an important role for these meiotic recombination factors in suppressing heterochromatic crossovers. Lastly, crossovers in flies mutant for Su(var)3-9 were mapped. Although a strong alleviation of crossover suppression in heterochromatic regions was expected, no changes in pericentromeric crossover distribution were observed in this mutant, indicating that this vital heterochromatin factor is dispensable to prevent crossovers in heterochromatin. These results indicate that the meiotic machinery plays a bigger role in suppressing crossovers than the chromatin state. |
| Babosha, V., Klimenko, N., Revel-Muroz, A., Tikhonova, E., Georgiev, P., Maksimenko, O. (2024). N-terminus of Drosophila melanogaster MSL1 is critical for dosage compensation. Elife, 13 PubMed ID: 39699942Summary: The male-specific lethal complex (MSL), which consists of five proteins and two non-coding roX RNAs, is involved in the transcriptional enhancement of X-linked genes to compensate for the sex chromosome monosomy in Drosophila XY males compared with XX females. The MSL1 and MSL2 proteins form the heterotetrameric core of the MSL complex and are critical for the specific recruitment of the complex to the high-affinity 'entry' sites (HAS) on the X chromosome. This study demonstrated that the N-terminal region of MSL1 is critical for stability and functions of MSL1. Amino acid deletions and substitutions in the N-terminal region of MSL1 strongly affect both the interaction with roX2 RNA and the MSL complex binding to HAS on the X chromosome. In particular, substitution of the conserved N-terminal amino-acids 3-7 in MSL1 (MSL1(GS)) affects male viability similar to the inactivation of genes encoding roX RNAs. In addition, MSL1(GS) binds to promoters such as MSL1(WT) but does not co-bind with MSL2 and MSL3 to X chromosomal HAS. However, overexpression of MSL2 partially restores the dosage compensation. Thus, the interaction of MSL1 with roX RNA is critical for the efficient assembly of the MSL complex on HAS of the male X chromosome. | Morledge-Hampton, B., Selvam, K., Chauhan, M., Goodman, A. G., Wyrick, J. J. (2025). Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency. Genome research, 35(2):257-267 PubMed ID: 39762049
Summary: Cyclobutane pyrimidine dimers (CPDs) are formed in DNA following exposure to ultraviolet (UV) light and are mutagenic unless repaired by nucleotide excision repair (NER). It is known that CPD repair rates vary in different genome regions owing to transcription-coupled NER and differences in chromatin accessibility; however, the impact of regional chromatin organization on CPD formation remains unclear. Furthermore, nucleosomes are known to modulate UV damage and repair activity, but how these damage and repair patterns are affected by the overarching chromatin domains in which these nucleosomes are located is not understood. Here, we generated a new CPD damage map in Drosophila S2 cells using CPD-seq and analyzed it alongside existing excision repair-sequencing (XR-seq) data to compare CPD damage formation and repair rates across five previously established chromatin types in Drosophila This analysis revealed that repair activity varies substantially across different chromatin types, whereas CPD formation is relatively unaffected. Moreover, distinct patterns of repair activity were observed in nucleosomes located in different chromatin types, which is shown to be owing to domain-specific differences in nucleosome repeat length (NRL). These findings indicate that NRL is altered in different chromatin types in Drosophila and that changes in NRL modulate the repair of UV lesions. |
| Fitz-James, M. H., Sabaris, G., Sarkies, P., Bantignies, F., Cavalli, G. (2025). Interchromosomal contacts between regulatory regions trigger stable transgenerational epigenetic inheritance in Drosophila. Mol Cell, 85(4):677-691.e676 PubMed ID: 39667935
Summary: Non-genetic information can be inherited across generations in a process known as transgenerational epigenetic inheritance (TEI). In Drosophila, hemizygosity of the Fab-7 regulatory element triggers inheritance of the histone mark H3K27me3 at a homologous locus on another chromosome, resulting in heritable epigenetic differences in eyePleiohomeotic and GAGA factor in the establishment and maintenance of TEI. These proteins function by recruiting the polycomb repressive complex 2 and by mediating interchromosomal chromatin contacts between Fab-7 and its homologous locus, respectively. Using an in vivo synthetic biology system to induce them, chromatin contacts alone can establish TEI, providing a mechanism by which hemizygosity of one locus can establish epigenetic memory at another distant locus in trans through chromatin contacts. | Colmenares, S. U., Tsukamoto, S., Hickmann, C., Brennan, L. D., Khavani, M., Mofrad, M., Karpen, G. (2024). Expanding the HP1a-binding consensus and molecular grammar for heterochromatin assembly. bioRxiv, PubMed ID: 39677692
Summary: The recruitment of Heterochromatin Protein 1 (HP1) partners is essential for heterochromatin assembly and function, yet knowledge regarding their organization in heterochromatin remains limited. Here we show that interactors engage the Drosophila HP1 (HP1a) dimer through a degenerate and expanded form of the previously identified PxVxL motif, which is now termed HP1a Access Codes (HACs). These HACs reside in disordered regions, possess high conservation among Drosophila homologs, and contain alternating hydrophobic residues nested in a cluster of positively charged amino acids. These findings and molecular dynamics simulations identify key electrostatic interactions that modulate HP1a-binding strength and provide a dramatically improved HP1a-binding consensus motif that can reveal protein partners and the molecular grammar involved in heterochromatin assembly. It is propose HP1a acts as a scaffold for other heterochromatin components containing HAC motifs, which in turn may regulate the function and higher order structure of the heterochromatin compartment. |
Thursday September 24th - Apoptosis and Autophagy |
| Li, M., Wang, Y., Wei, X., Cai, W. F., Wu, J., Zhu, M., Wang, Y., Liu, Y. H., Xiong, J., Qu, Q., Chen, Y., Tian, X., Yao, L., Xie, R., Li, X., Chen, S., Huang, X., Zhang, C., Xie, C., Wu, Y., Xu, Z., Zhang, B., Jiang, B., Wang, Z. C., Li, Q., Li, G., Lin, S. Y., Yu, L., Piao, H. L., Deng, X., Han, J., Zhang, C. S., Lin, S. C. (2024). AMPK targets PDZD8 to trigger carbon source shift from glucose to glutamine. Cell Res, 34(10):683-706 PubMed ID: 38898113
Summary: The shift of carbon utilization from primarily glucose to other nutrients is a fundamental metabolic adaptation to cope with decreased blood glucose levels and the consequent decline in glucose oxidation. AMP-activated protein kinase (AMPK) plays crucial roles in this metabolic adaptation. However, the underlying mechanism is not fully understood. This study shows that PDZ domain containing 8 (PDZD8), which this study identified as a new substrate of AMPK activated in low glucose, is required for the low glucose-promoted glutaminolysis. AMPK phosphorylates PDZD8 at threonine 527 (T527) and promotes the interaction of PDZD8 with and activation of glutaminase 1 (GLS1), a rate-limiting enzyme of glutaminolysis. In vivo, the AMPK-PDZD8-GLS1 axis is required for the enhancement of glutaminolysis as tested in the skeletal muscle tissues, which occurs earlier than the increase in fatty acid utilization during fasting. The enhanced glutaminolysis is also observed in macrophages in low glucose or under acute lipopolysaccharide (LPS) treatment. Consistent with a requirement of heightened glutaminolysis, the PDZD8-T527A mutation dampens the secretion of pro-inflammatory cytokines in macrophages in mice treated with LPS. Together, this study haa revealed an AMPK-PDZD8-GLS1 axis that promotes glutaminolysis ahead of increased fatty acid utilization under glucose shortage. | El Fissi, N., Rosenberger, F. A., Chang, K., Wilhalm, A., Barton-Owen, T., Hansen, F. M., Golder, Z., Alsina, D., Wedell, A., Mann, M., Chinnery, P. F., Freyer, C., Wredenberg, A. (2024). Preventing excessive autophagy protects from the pathology of mtDNA mutations in Drosophila melanogaster. Nat Commun, 15(1):10719 PubMed ID: 39715749
Summary: Aberration of mitochondrial function is a shared feature of many human pathologies, characterised by changes in metabolic flux, cellular energetics, morphology, composition, and dynamics of the mitochondrial network. While some of these changes serve as compensatory mechanisms to maintain cellular homeostasis, their chronic activation can permanently affect cellular metabolism and signalling, ultimately impairing cell function. This study used a Drosophila melanogaster model expressing a proofreading-deficient mtDNA polymerase (POLγ(exo-)) in a genetic screen to find genes that mitigate the harmful accumulation of mtDNA mutations. Citical pathways were identified associated with nutrient sensing, insulin signalling, mitochondrial protein import, and autophagy that can rescue the lethal phenotype of the POLγ(exo-) flies. Rescued flies, hemizygous for dilp1, atg2, tim14 or melted, normalise their autophagic flux and proteasome function and adapt their metabolism. Mutation frequencies remain high with the exception of melted-rescued flies, suggesting that melted/γ(exo-) larvae with the autophagy activator rapamycin aggravates their lethal phenotype, highlighting that excessive autophagy can significantly contribute to the pathophysiology of mitochondrial diseases. Moreover, this study showed that the nucleation process of autophagy is a critical target for intervention. |
| Chen, Y., Hu, J., Zhao, P., Fang, J., Kuang, Y., Liu, Z., Dong, S., Yao, W., Ding, Y., Wang, X., Pan, Y., Wu, J., Zhao, J., Yang, J., Xu, Z., Liu, X., Zhang, Y., Wu, C., Zhang, L., Fan, M., Feng, S., Hong, Z., Yan, Z., Xia, H., Tang, K., Yang, B., Liu, W., Sun, Q., Mei, K., Zou, W., Huang, Y., Feng, D., Yi, C. (2025). Rpl12 is a conserved ribophagy receptor. Nat Cell Biol, 27(3):477-492 PubMed ID: 39934334
Summary: Ribophagy is a selective autophagic process that regulates ribosome turnover. Although NUFIP1 has been identified as a mammalian receptor for ribophagy, its homologues do not exist in yeast and nematodes. This study demonstrated that Rpl12, a ribosomal large subunit protein, functions as a conserved ribophagy receptor in multiple organisms. Disruption of Rpl12-Atg8s binding leads to significant accumulation of ribosomal proteins and rRNA, while Atg1-mediated Rpl12 phosphorylation enhances its association with Atg11, thus triggering ribophagy during starvation. Ribophagy deficiency accelerates cell death induced by starvation and pathogen infection, leading to impaired growth and development and a shortened lifespan in both Caenorhabditis elegans and Drosophila melanogaster. Moreover, ribophagy deficiency results in motor impairments associated with ageing, while the overexpression of RPL12 significantly improves movement defects induced by starvation, ageing and Aβ accumulation in fly models. These findings suggest that Rpl12 functions as a conserved ribophagy receptor vital for ribosome metabolism and cellular homeostasis (Chen, 2025). | Wang, L., Yi, S., Zhang, S., Tsai, Y. T., Cheng, Y. H., Lin, Y. T., Lin, C. C., Lee, Y. H., Wang, H., Ho, M. S. (2025). New Atg9 Phosphorylation Sites Regulate Autophagic Trafficking in Glia. ASN Neuro, 17(1):2443442 PubMed ID: 39807990
Summary: Previous work identified a role for dAuxilin (dAux), the fly homolog of Cyclin G-associated kinase, in glial autophagy contributing to Parkinson's disease (PD). To further dissect the mechanism, evidence is presented that lack of glial dAux enhanced the phosphorylation of the autophagy-related protein Atg9 at two newly identified threonine residues, T62 and T69. The enhanced Atg9 phosphorylation in the absence of dAux promotes autophagosome formation and Atg9 trafficking to the autophagosomes in glia. Whereas the expression of the non-phosphorylatable Atg9 variants suppresses the lack of dAux-induced increase in both autophagosome formation and Atg9 trafficking to autophagosome, the expression of the phosphomimetic Atg9 variants restores the lack of Atg1-induced decrease in both events. In relation to pathophysiology, Atg9 phosphorylation at T62 and T69 contributes to dopaminergic neurodegeneration and locomotor dysfunction in a Drosophila PD model. Notably, increased expression of the master autophagy regulator Atg1 promotes dAux-Atg9 interaction. Thus, this study has identified a dAux-Atg1-Atg9 axis relaying signals through the Atg9 phosphorylation at T62 and T69; these findings further elaborate the mechanism of dAux regulating glial autophagy and highlight the significance of protein degradation pathway in glia contributing to PD. |
| Sadanandappa, M. K., Bosco, G. (2024). Olfactory inputs regulate Drosophila melanogaster oogenesis. J Exp Biol, 227(24) PubMed ID: 39660407
Summary: Drosophila female germline development and maintenance require both local stem cell niche signaling and systemic regulation. This study shows the indispensable function of the Drosophila melanogaster olfactory circuit in normal oogenesis and fecundity. Lack of olfactory inputs during development causes a reduction in germline stem cells. Although germline stem cells proliferate normally, the germline cysts undergo caspase-mediated apoptosis, leading to decreased follicle production and egg-laying in flies with defective olfaction. Strikingly, activation of olfactory circuits is sufficient to boost egg production, demonstrating that chemosensory-activated brain-derived inputs promote gamete development. Given the energy demands of oogenesis and its direct consequence on fitness, it is proposed that olfactory-stimulated systemic regulation evolved tightly with downstream diet-responsive pathways to control germline physiology in response to nutritional status. Additionally, these findings raise the possibility that sensory-mediated stem cell maintenance is a generalizable mechanism spanning a myriad of neuronal circuits, systems and species. | Bhadauriya, P., Onkar, A., Nagarajan, K., Angamuthu Karuppusamy, K., Ganesh, S., Agarwal, S. (2025). Glycogen synthase is required for heat shock-mediated autophagy induction in neuronal cells. Biology open, 14(2) PubMed ID: 39912200
Summary: Autophagy is an essential cellular process that facilitates the degradation of aggregated proteins and damaged organelles to maintain cellular homeostasis and promote cell survival. Recent studies have indicated a direct role for glycogen synthase (GS) in activating neuronal autophagy and in conferring protection against cytotoxic misfolded proteins. Since heat shock induces protein misfolding and autophagy is an essential component of the heat shock response that clears the misfolded proteins, this study looked at the possible role of GS in heat shock response pathways in neuronal cells. An increase was demonstrated in the activity and level of GS and a concomitant increase in the glycogen level during the heat shock and post-heat shock recovery period. These changes had a direct correlation with autophagy induction. It was demonstrated that heat shock transcription factor 1 regulates the level and activation of GS during heat shock and that GS is essential for the induction of autophagy during heat stress in neuronal cells. Intriguingly, the partial knock-down of GS led to increased death due to heat shock in neuronal cells and Drosophila. This study offers a novel insight into the role of GS and glycogen metabolic pathways in heat shock response in neuronal cells. |
Monday September 21st - Evolution |
| Edwards, S., Naundrup, A., Becher, P. G., De Fine Licht, H. H. (2025). Patterns of genotype-specific interactions in an obligate host-specific insect pathogenic fungus. J Evol Biol, 38(2):225-239 PubMed ID: 39671697
Summary: Host-pathogen infections and possible effects on co-evolutionary patterns depend on the genotypes of both host and pathogen. Obligate fungal pathogens of plants are often characterized by host-pathogen genotype-by-genotype (GxG) interactions, but whether these patterns exist in obligate insect fungal pathogens is unclear. This study took advantage of the obligate insect pathogenic fungus Entomophthora muscae, where individual isolates are specific to different dipteran host species in nature but can cross-infect multiple fly species in the laboratory. Three new isolates of E. muscae were collected from Drosophila species. Phylogenetic analysis showed that Drosophila-isolated E. muscae represents a distinct geographically widespread Drosophila lineage compared to the house fly (Musca domestica) or Delia species-isolated E. muscae. The three new E. muscae isolates from Drosophila spp. were used together with a genetically distinct E. muscae isolate from house flies, and their virulence was assessed in a cross-infection experiment using one house fly, three Drosophila suzukii, and two D. melanogaster genotypes as hosts. All fungal isolates successfully infected hosts, induced behavioural manipulation, sporulated in all fly hosts, and differed in virulence between host genotypes, revealing GxG interactions. While house flies were most susceptible to fungal infection with 99% mortality, a lower virulence of 49% and 25% mortality was found in D. melanogaster and D. suzukii genotypes, respectively. Furthermore, all isolates harboured a specific mycovirus (family Iflaviridae), but co-phylogenetic branching patterns did not support fungus-virus co-speciation. This study has shown that the genetic makeup of both fungal pathogen and fly host influence E. muscae infectivity, confirming GxG interactions in obligate fly fungal pathogens. | Jezovit, J. A., Levine, J. D. (2025). Chemical signals and social structures strengthen sexual isolation in Drosophila pseudoobscura. Communications biology, 8(1):76 PubMed ID: 39824898
Summary: Species that coexist in hybrid zones sexually isolate through reproductive character displacement, a mechanism that favours divergence between species. In Drosophila, behavioural and physiological traits discourage heterospecific mating between species. Recently, social network analysis revealed flies produce strain-specific and species-specific social structures. A gene, degrees of kevin bacon (dokb) has also been discovered that accounts for differences in social structures between flies. Why differences in social structures exist between drosophilids is currently unknown. This study shows through an experimental evolution study that six generations of selection in experimental sympatry led to the divergence of social structures measured in Drosophila pseudoobscura and Drosophila persimilis flies. The frequency of hybrid offspring decreased within a few generations, suggesting social structures are associated with the sexual isolation of species. This study also reports increased species' differences in the concentration of the cuticular hydrocarbon 5, 9-pentacosadiene after six generations of selection. The mean concentration of this compound converged in female flies of both species and diverged in male flies of both species, suggesting a quantitative link between increased sexual dimorphism and sexual isolation. These results suggest that chemical signals, together with social structures, increase the sexual isolation between species in hybrid zones. |
| Cherezov, R. O., Vorontsova, J. E., Kuvaeva, E. E., Akishina, A. A., Zavoloka, E. L., Simonova, O. B. (2025). The lawc gene emerged de novo from conserved genomic elements and acquired a broad expression pattern in Drosophila. J Genet Genomics, 52(7):901-914 PubMed ID: 39733859
Summary: It has recently become evident that the de novo emergence of genes is widespread and documented for a variety of organisms. De novo genes frequently emerge in proximity to existing genes, forming gene overlaps. This study presents an analysis of the evolutionary history of a putative de novo gene, lawc, which overlaps with the conserved Trf2 gene, which encodes a general transcription factor in Drosophila melanogaster. lawc emerged approximately 68 million years ago in the 5'-untranslated region (UTR) of Trf2 and displays an extensive spatiotemporal expression pattern. One of the most remarkable features of the lawc evolutionary history is that its emergence was facilitated by the engagement of Drosophilidae-specific short, highly conserved regions located in Trf2 introns. This represents a unique example of putative de novo gene birth involving conserved DNA regions localized in introns of conserved genes. The observed lawc expression pattern may be due to the overlap of lawc with the 5'-UTR of Trf2. This study not only enriches understanding of gene evolution but also highlights the complex interplay between genetic conservation and innovation. | Jean-Francois, F., Pratibha, S., Baptiste, R., Jean-Pierre, F., Jerome, C., Deepa, A., Claude, E. (2025). Is Drosophila Larval Competition Involved in Incipient Speciation? J Chem Ecol, 51(1):2 PubMed ID: 39841299
Summary: Geographical, ethological, temporal and ecological barriers can affect interbreeding between populations deriving from an ancestral population, this progressively leading to speciation. A rare case of incipient speciation currently occurs between Drosophila melanogaster populations sampled in Zimbabwe (Z) and all other populations (M). This phenomenon was initially characterized by Z females refusing to mate with M males. Despite the fact that Z and M flies produce different amounts of cuticular pheromones, their manipulation and that of other sensory signals exchanged during courtship behavior only marginally rescued the behavioral isolation. To further explore the putative mechanisms involved in this phenomenon, the fecundity in matings between Z and M flies was assessed. Then, the reproduction and survival in adults resulting of co-cultured Z and M larvae was measured. In these two experiments, Z flies rarely emerged. Z and M larvae produced different amounts of food-derived metabolites which were altered in co-culture condition. This maybe related to the different bacteria composition in the gut and body of Z and M flies. However, the mating behavior of co-cultured flies did not change and their cuticular pheromone profile was slightly altered. Thus, the Z/M larval competition could reinforce the barriers induced by gametic and behavioral isolation processes on this incipient speciation phenomenon. |
| Jarvis, W. M. C., Careau, V., Rundle, H. D. (2025). Divergence in genetic (co)variances and the alignment of gmax with phenotypic divergence. Evolution; international journal of organic evolution, 79(4):597-610 PubMed ID: 39841166
Summary: To better understand the sources of biological diversity in nature, information is needed on the mechanisms underlying population divergence. Biological systems with patterns of naturally occurring adaptive variation among populations can provide insight into the genetic architecture of diverging traits and the influence of genetic constraints on responses to selection. Using a system of reproductive character displacement in the North American mushroom-feeding fly Drosophila subquinaria, this study assessed patterns of genetic (co)variance among a suite of chemical signaling traits and divergence in this pattern among populations. D. subquinaria exhibits stronger reproductive isolation against the closely related Drosophila recens in sympatry, where both female mating preferences and male chemical signaling traits have diverged from the ancestral allopatric populations. Three wild populations were collected from each region and, in the lab, the phenotypic divergence in these traits were characterized, as well as the additive genetic (co)variance structure (G-matrix), via replicate breeding designs. Divergence was found between allopatric and sympatric D. subquinaria in the shape and size of the G-matrix, and the leading axis of genetic variance (gmax) had changed in sympatry to come into alignment with the primary axis of phenotypic divergence between the sympatric and allopatric regions. | Rohner, P. T., Berger, D. (2025). Macroevolution along developmental lines of least resistance in fly wings. Nat Ecol Evol, 9(4):639-651 PubMed ID: 39920350
Summary: Evolutionary change requires genetic variation, and a reigning paradigm in biology is that rates of microevolution can be predicted from estimates of available genetic variation within populations. However, the accuracy of such predictions should decay on longer evolutionary timescales, as the influence of genetic constraints diminishes. This study shows that intrinsic developmental variability and standing genetic variation in wing shape in two distantly related flies, Drosophila melanogaster and Sepsis punctum, are aligned and predict deep divergence in the dipteran phylogeny, spanning >900 taxa and 185 million years. This alignment cannot be easily explained by constraint hypotheses unless most of the quantified standing genetic variation is associated with deleterious side effects and is effectively unusable for evolution. However, phenotyping of 71 genetic lines of S. punctum revealed no covariation between wing shape and fitness, lending no support to this hypothesis. Little evidence was found for genetic constraints on the pace of wing shape evolution along the dipteran phylogeny. Instead, correlational selection related to allometric scaling, simultaneously shaping developmental variability and deep divergence in fly wings, emerges as a potential explanation for the observed alignment. This suggests that pervasive natural selection has the potential to shape developmental architectures of some morphological characters such that their intrinsic variability predicts their long-term evolution. |
Friday September 18th - Adult physiology and Metabolism |
| Yadav, S., Pan, X., Li, S., Martin, P. L., Hoang, N., Chen, K., Karhadkar, A., Malhotra, J., Zuckerman, A. L., Munan, S., Klose, M. K., Wang, L., Cracan, V., Parkhitko, A. A. (2025). Tissue-specific modulation of NADH consumption as an anti-aging intervention in Drosophila. JbioRxiv, PubMed ID: 39829793
Summary: Aging is characterized by extensive metabolic dysregulation. Redox coenzyme nicotinamide adenine dinucleotide (NAD) can exist in oxidized (NAD(+)) or reduced (NADH) states, which together form a key NADH/NAD(+) redox pair. Total levels of NAD decline with age in a tissue-specific manner, thereby playing a significant role in the aging process. Supplementation with NAD precursors boosts total cellular NAD levels and provides some therapeutic benefits in human clinical trials. However, supplementation studies cannot determine tissue-specific effects of an altered NADH/NAD(+) ratio. This study created transgenic Drosophila expressing a genetically encoded xenotopic tool LbNOX to directly manipulate the cellular NADH/NAD(+) ratio. LbNOX expression in Drosophila was shown to impact both NAD(H) and NADP(H) metabolites in a sex-specific manner. LbNOX rescues neuronal cell death induced by the expression of mutated alpha-B crystallin in the Drosophila eye, a widely used system to study reductive stress. Utilizing LbNOX, targeting redox NAD metabolism in different tissues may have drastically different outcomes, as the expression of LbNOX solely in the muscle is much more effective for rescuing paraquat-induced oxidative stress compared to whole-body expression. Excitingly, we demonstrate that perturbing NAD(P) metabolism in non-neuronal tissues is sufficient to rejuvenate sleep profiles in aged flies to a youthful state. In summary, the xenotopic tool LbNOX was used to identify tissues and metabolic processes which benefited the most from the modulation of the NAD metabolism thereby highlighting important aspects of rebalancing the NAD and NADP pools, all of which can be translated into novel designs of NAD-related human clinical trials. | Alaraby, M., Abass, D., Gutierrez, J., Velazquez, A., Hernandez, A., Marcos, R. (2024). Reproductive Toxicity of Nanomaterials Using Silver Nanoparticles and Drosophila as Models. Molecules, 29(23) PubMed ID: 39683959
Summary: Reproductive toxicity is of special concern among the harmful effects induced by environmental pollutants; consequently, further studies on such a topic are required. To avoid the use of mammalians, lower eukaryotes like Drosophila are viable alternatives. This study addresses the gap in understanding the link between reproductive adverse outcomes and the presence of pollutants in reproductive organs by using Drosophila. Silver nanoparticles (AgNPs) were selected for their ease of internalization, detection, and widespread environmental presence. Both male and female flies were exposed to AgNPs for one week. Internalization and bioaccumulation of AgNPs in organs were assessed using transmission electron microscopy, confocal microscopy, and inductively coupled plasma mass spectrometry. Substantial accumulation of AgNPs in the gastrointestinal tract, Malpighian tubules, hemolymph, reproductive organs (ovaries and testes), and gametes were observed. The highest AgNP content was observed in testes. Exposure to AgNPs reduced ovary size and fecundity, though fertility and gender ratios of the offspring were unaffected. Significant deregulation of reproductive-related genes was observed, particularly in males. These findings underscore the utility of Drosophila as a model for evaluating reproductive hazards posed by AgNP exposure. The ease of AgNP internalization in Drosophila reproductive targets could be extrapolated to mammalians, raising concerns about the potential impacts of nanoparticle exposure on reproduction toxicity in humans. |
| Bettinazzi, S., Liang, J., Rodriguez, E., Bonneau, M., Holt, R., Whitehead, B., Dowling, D. K., Lane, N., Camus, M. F. (2024). Assessing the role of mitonuclear interactions on mitochondrial function and organismal fitness in natural Drosophila populations. Evol Lett, 8(6):916-926 PubMed ID: 39677574
Summary: Mitochondrial function depends on the effective interactions between proteins and RNA encoded by the mitochondrial and nuclear genomes. Evidence suggests that both genomes respond to thermal selection and promote adaptation. However, the contribution of their epistatic interactions to life history phenotypes in the wild remains elusive. This study investigated the evolutionary implications of mitonuclear interactions in a real-world scenario that sees populations adapted to different environments, altering their geographical distribution while experiencing flow and admixture. A Drosophila melanogaster panel was created with replicate native populations from the ends of the Australian east-coast cline, into which the mtDNA haplotypes were substituted that were either predominant or rare at each cline-end, thus creating putatively mitonuclear matched and mismatched populations. The results suggest that mismatching may impact phenotype, with populations harboring the rarer mtDNA haplotype suffering a trade-off between aerobic capacity and key fitness aspects such as reproduction, growth, and survival. The significance of mitonuclear interactions as modulators of life history phenotypes is discussed in the context of future adaptation and population persistence. | Wu, S. C., Chen, Y. J., Su, S. H., Fang, P. H., Liu, R. W., Tsai, H. Y., Chang, Y. J., Li, H. H., Li, J. C., Chen, C. H. (2025). Dysfunctional BCAA degradation triggers neuronal damage through disrupted AMPK-mitochondrial axis due to enhanced PP2Ac interaction. Communications biology, 8(1):105 PubMed ID: 39838082
Summary: Metabolic and neurological disorders commonly display dysfunctional branched-chain amino acid (BCAA) metabolism, though it is poorly understood how this leads to neurological damage. This was investigated by generating Drosophila mutants lacking BCAA-catabolic activity, resulting in elevated BCAA levels and neurological dysfunction, mimicking disease-relevant symptoms. The findings reveal a reduction in neuronal AMP-activated protein kinase (AMPK) activity, which disrupts autophagy in mutant brain tissues, linking BCAA imbalance to brain dysfunction. Mechanistically,excess BCAA-induced mitochondrial reactive oxygen species (ROS) was shown to trigger the binding of protein phosphatase 2 A catalytic subunit (PP2Ac) to AMPK, suppressing AMPK activity. This initiated a dysregulated feedback loop of AMPK-mitochondrial interactions, exacerbating mitochondrial dysfunction and oxidative neuronal damage. This study identifies BCAA imbalance as a critical driver of neuronal damage through AMPK suppression and autophagy dysfunction, offering insights into metabolic-neuronal interactions in neurological diseases and potential therapeutic targets for BCAA-related neurological conditions. |
| Wang, F., Yang, P., Xu, L., Han, X., Zhang, M. (2025). Effects of cadmium on female Drosophila melanogaster and its transgenerational inheritance effects. J Environ Manage, 374:124076 PubMed ID: 39818074
Summary: Cadmium (Cd) is a silvery-white and shiny heavy metal that is common in daily life and can adversely affect the development, lifespan, and reproduction of organisms. In this study, Drosophila melanogaster (F(0)) were cultured from eggs to adults in medium containing different Cd concentrations (0, 2.25, and 4.5 mg/kg), and offspring (F(1)-F(4) generations) were cultured in standard medium. The morphology of the ovaries of female flies under Cd stress changed, apoptosis occurred, fertility decreased, and the levels of 20-Hydroxyecdysone and vitellogenin decreased significantly. These changes were more significant under high-concentration treatment. In addition, the inhibitory effects of Cd on reproduction-related genes (spook, phantom, disembodies, shadow, shade, ECR, vg, and Kr-h1) in F(0) female flies could transmit to two or three generations. Cd exposure also induced increased expression of miR-927 and mediated its transgenerational inheritance. These results indicate that damage to the ovaries and the changes in related-genes expressions of female flies induced by Cd stress can be transmitted to offspring and may be related to changes in miRNA expression in Drosophila. The transgenerational inheritance effects of heavy metals on organisms and their potential risks to future ecosystems deserve attention and reassess. | Benedetti, L., Fan, R., Weigel, A. V., Moore, A. S., Houlihan, P. R., Kittisopikul, M., Park, G., Petruncio, A., Hubbard, P. M., Pang, S., Xu, C. S., Hess, H. F., Saalfeld, S., Rangaraju, V., Clapham, D. E., De Camilli, P., Ryan, T. A., Lippincott-Schwartz, J. (2025). Periodic ER-plasma membrane junctions support long-range Ca(2+) signal integration in dendrites. Cell, 188(2):484-500.e422 PubMed ID: 39708809
Summary: Neuronal dendrites must relay synaptic inputs over long distances, but the mechanisms by which activity-evoked intracellular signals propagate over macroscopic distances remain unclear. This study discovered a system of periodically arranged endoplasmic reticulum-plasma membrane (ER-PM) junctions tiling the plasma membrane of dendrites at ~1 μm intervals, interlinked by a meshwork of ER tubules patterned in a ladder-like array. Populated with Junctophilin-linked plasma membrane voltage-gated Ca(2+) channels and ER Ca(2+)-release channels (ryanodine receptors), ER-PM junctions are hubs for ER-PM crosstalk, fine-tuning of Ca(2+) homeostasis, and local activation of the Ca(2+)/calmodulin-dependent protein kinase II. Local spine stimulation activates the Ca(2+) modulatory machinery, facilitating signal transmission and ryanodine-receptor-dependent Ca(2+) release at ER-PM junctions over 20 μm away. Thus, interconnected ER-PM junctions support signal propagation and Ca(2+) release from the spine-adjacent ER. The capacity of this subcellular architecture to modify both local and distant membrane-proximal biochemistry potentially contributes to dendritic computations. |
Wednesday September 16th - Signaling |
| Kinoshita, J., Kinoshita, Y., Nomura, T., Inoue, Y. H. (2024). Macrophage-like Blood Cells Are Involved in Inter-Tissue Communication to Activate JAK/STAT Signaling, Inducing Antitumor Turandot Proteins in Drosophila Fat Body via the TNF-JNK Pathway. Int J Mol Sci, 25(23) PubMed ID: 39684820
Summary: Turandot (Tot) family proteins (consisting of 8 members), which are induced via the JAK/STAT pathway after infection, also suppress lymph gland tumors in Drosophila mxc(mbn1) mutant larvae. The potential role of hemocytes (immune blood cells) in Tot induction in tumor-bearing mutants was examined via immunostaining and RNAi experiments. Normal hemocytes transplanted into mutant larvae were recruited to the tumor and fat body (FB), suggesting that these cells transmit tumor-related information. The transplanted hemocytes ectopically expressed Unpaired3 (Upd3), which is necessary for the activation of JAK/STAT. Eiger, a Drosophila tumor necrosis factor (TNF) ortholog, was highly expressed in tumors. Depletion of the Eiger receptor in hemocytes reduced Tot levels and eventually enhanced tumor growth. The c-Jun N-terminal kinase (JNK) pathway, acting downstream of the receptor, was also activated in the hemocytes of mutants. Downregulation of the JNK pathway in hemocytes inhibited Tot induction, leading to enhanced tumor growth. These results suggest that upd3 expression in hemocytes depends on the Eiger-JNK pathway. It is proposed that after Eiger activates the JNK pathway in hemocytes present on the tumor, cells expressing Upd3 are recruited to the FB. Upd3 then activates JAK/STAT to induce the expression of antitumor proteins. This study highlights the intricate communication between tissues via blood cells during tumor suppression. | Garcia-Alonso, L. (2024). Fasciclin 2 functions as an expression-level switch on EGFR to control organ shape and size in Drosophila. PLoS One, 19(12):e0309891 PubMed ID: 39705210
Summary: Fasciclin 2 (Drosophila NCAM) is a homophilic Cell Adhesion Molecule expressed at moderate levels in the proliferating epithelial cells of imaginal discs, where it engages EGFR in a cell autonomous auto-stimulatory loop that promotes growth along larval development. In addition, Fasciclin 2 is expressed at high levels in the pre-differentiating cells of imaginal discs. Gain-of-function genetic analysis shows that Fasciclin 2 acts as a non-cell autonomous repressor of EGFR when high expression levels are induced during imaginal disc growth. Loss-of-function genetic analysis shows that this Fasciclin 2 functional facet is required at the end of larval development and it is mediated by interaction with IgCAMs CG15630 (Fipi) and CG33543 (Elff). Thus, Fasciclin 2 bears two complementary functional roles which correspond with different levels of expression. The combined results from loss- and gain-of-function analyses suggest a scenario where the Fasciclin 2/EGFR cell autonomous auto-stimulatory loop promotes cell proliferation until reaching a Fasciclin 2 expression threshold where its non-cell autonomous function stops growth. NCAM-type proteins have been shown to require homophilic cis interactions for trans binding homophilic functional adhesion, and it has been proposed that they are required to build membrane molecular zippers. Thus, Fas2 may be incorporated in the plasma membrane as a growing zipper during imaginal disc cell proliferation. Thus, cellular integration of Fasciclin 2 autonomous and non-cell autonomous signaling from neighbor cells may be a key regulator component to orchestrate the rate of intercalary cell proliferation and the final size and shape of an organ. |
| Arias, R. A., Tomlinson, A. (2025). Decoding a Cell's Fate: How Notch and receptor tyrosine kinase signals specify the Drosophila R7 photoreceptor. Dev Biol, 519:21-29 PubMed ID: 39653132
Summary: The process by which the Drosophila R7 photoreceptor is specified has become a classic model for understanding how cell-cell signals direct cell fates. In the R7 precursor cell, both the Notch and receptor tyrosine kinase (RTK) signaling pathways are active, and the information they encode directs the specification of the R7 photoreceptor identity. In this process, Notch performs three distinct functions: it both opposes and promotes the actions of the RTK pathway to specify the photoreceptor fate, and it determines the type of photoreceptor that is specified. The RTK pathway drives transcription of phyl - a gene expression necessary for photoreceptor specification. Notch activity is shown to induce transcription of the yan gene which encodes a transcriptional repressor of phyl. This defines an antagonism between the two pathways, with RTK promoting and Notch opposing phyl transcription. Previous work showed that Notch activity supplies Sevenless to the R7 precursor to allow the RTK pathway hyperactivation required to overcome the Notch repression, and we now identify the regulation of Yan activity as a site of integration of RTK and Notch signaling pathways. Once the cell is specified as a photoreceptor, the third Notch function then prevents seven-up (svp) transcription. The Svp transcription factor directs the R1/6 photoreceptor fate, and the prevention of its expression ensures the default R7 specification. | Zhang, J., Tsutsui, Y., Li, H., Li, T., Wang, Y., Laraki, S., Alarcon-Frias, S., Stayrook, S. E., Klein, D. E. (2025). Structural basis for the interaction between the Drosophila RTK Sevenless (dROS1) and the GPCR BOSS. Nature communications, 16(1):808 PubMed ID: 39827240
Summary: Sevenless, the Drosophila homologue of ROS1 (herein, dROS1) is a receptor tyrosine kinase (RTK) essential for the differentiation of Drosophila R7 photoreceptor cells. Activation of dROS1 is mediated by binding to the extracellular region (ECR) of the GPCR (G protein coupled receptor) BOSS (Bride Of Sevenless) on adjacent cells. Activation of dROS1 by BOSS leads to subsequent downstream signaling pathways including SOS (Son of Sevenless). However, the physical basis for how dROS1 interacts with BOSS has long remained unknown. This study provides a cryo-EM structure of the dROS1 extracellular region, which mediates ligand binding. The extracellular region of dROS1 adopts a folded-over conformation stabilized by an N-terminal domain comprised of two disulfide stapled helical hairpins. The interacting binding epitopes on both dROS1 and BOSS was further narrowed down using hydrogen-deuterium exchange mass spectrometry (HDX-MS). This includes beta-strands in dROS1's third Fibronectin type III (FNIII) domain and a C-terminal peptide in the BOSS ECR. Mutagenesis studies, coupled with AlphaFold complex predictions, support a binding interaction mediated by a hydrophobic interaction and beta-strand augmentation between these regions. These findings provide a fundamental understanding of the regulatory function of dROS1 and further provide mechanistic insight into the human ortholog and oncogene ROS1. |
| Nelson, J. O., Slicko, A., Raz, A. A., Yamashita, Y. M. (2025). Insulin signaling regulates R2 retrotransposon expression to orchestrate transgenerational rDNA copy number maintenance. Nature communications, 16(1):399 PubMed ID: 39755735
Summary: Preserving a large number of essential yet highly unstable ribosomal DNA (rDNA) repeats is critical for the germline to perpetuate the genome through generations. Spontaneous rDNA loss must be countered by rDNA copy number (CN) expansion. Germline rDNA CN expansion is best understood in Drosophila melanogaster, which relies on unequal sister chromatid exchange (USCE) initiated by DNA breaks at rDNA. The rDNA-specific retrotransposon R2 responsible for USCE-inducing DNA breaks is typically expressed only when rDNA CN is low to minimize the danger of DNA breaks; however, the underlying mechanism of R2 regulation remains unclear. This study identifired the insulin receptor (InR) as a major repressor of R2 expression, limiting unnecessary R2 activity. Through single-cell RNA sequencing, male germline stem cells (GSCs), the major cell type that undergoes rDNA CN expansion, were found to have reduced InR expression when rDNA CN is low. Reduced InR activity in turn leads to R2 expression and CN expansion. Dietary manipulation was found to alters R2 expression and rDNA CN expansion activity. This work reveals that the insulin pathway integrates rDNA CN surveying with environmental sensing, revealing a potential mechanism by which diet exerts heritable changes to genomic content. | Nelson, K. A., Lenhart, K. F., Anllo, L., DiNardo, S. (2025). The Drosophila hematopoietic niche assembles through collective cell migration controlled by neighbor tissues and Slit-Robo signaling. eLife, 13 PubMed ID: 39750120
Summary: Niches are often found in specific positions in tissues relative to the stem cells they support. Consistency of niche position suggests that placement is important for niche function. However, the complexity of most niches has precluded a thorough understanding of how their proper placement is established. To address this, the formation of a genetically tractable niche, the Drosophila Posterior Signaling Center (PSC) was investigated, the assembly of which had not been previously explored. This niche controls hematopoietic progenitors of the lymph gland (LG). PSC cells were previously shown to be specified laterally in the embryo, but ultimately reside dorsally, at the LG posterior. Using live-imaging, this study showed that PSC cells migrate as a tight collective and associate with multiple tissues during their trajectory to the LG posterior. Slit emanating from two extrinsic sources, visceral mesoderm and cardioblasts (heart progenitors), is required for the PSC to remain a collective, and for its attachment to cardioblasts during migration. Without proper Slit-Robo signaling, PSC cells disperse, form aberrant contacts, and ultimately fail to reach their stereotypical position near progenitors. Thisr work characterizes a novel example of niche formation and identifies an extrinsic signaling relay that controls precise niche positioning. |
Monday September 14th - Larval and Adult Neural Development, Structure, and Function |
| Zhang, S., Li, K., Luo, Z., Xu, M., Zheng, S. (2025). A Bio-Inspired Visual Neural Model for Robustly and Steadily Detecting Motion Directions of Translating Objects Against Variable Contrast in the Figure-Ground and Noise Interference. Biomimetics (Basel), 10(1) PubMed ID: 39851767
Summary: At present, the bio-inspired visual neural models have made significant achievements in detecting the motion direction of the translating object. The responses of the lobula plate tangential cell (LPTC) neurons of Drosophila are robust and stable in the face of variable contrast in the figure-ground and environmental noise interference, which provides an excellent paradigm for addressing these challenges. To resolve these challenges, a bio-inspired visual neural model is proposed, which consists of four stages. 1. The photoreceptors (R1-R6) are utilized to perceive the change in luminance. 2. The change in luminance is divided into parallel ON and OFF pathways based on the lamina monopolar cell (LMC), and the spatial denoising and the spatio-temporal lateral inhibition (LI) can suppress environmental noise and improve motion boundaries. 3. The non-linear instantaneous feedback mechanism in divisive contrast normalization is adopted to reduce local contrast sensitivity; further, the parallel ON and OFF contrast pathways are activated. 4. The parallel motion and contrast pathways converge on the LPTC in the lobula complex. This study draws four conclusions. 1. The effectiveness of the contrast neural computation and the spatial denoising mechanism is verified by the ablation study. 2. This model can robustly detect the motion direction of the translating object against variable contrast in the figure-ground. 3. This model can effectively reduce the fluctuation in this model response against variable contrast in the figure-ground and environmental noise interference. 4. The robustness and stability of this model are further verified by comparing other early visual pre-processing mechanisms and engineering denoising methods. This model can robustly and steadily detect the motion direction of the translating object under variable contrast in the figure-ground and environmental noise interference (Note: This abstract was heavily edited). | Neuman, S. D., Thakur, R. S., Gratz, S. J., O'Connor-Giles, K. M., Bashirullah, A. (2024). Neurodegenerative and neurodevelopmental roles for bulk lipid transporters VPS13A and BLTP2 in movement disorders. bioRxiv, PubMed ID: 39803515
Summary: Bridge-like lipid transfer proteins (BLTPs) mediate bulk lipid transport at membrane contact sites. Mutations in BLTPs are linked to both early-onset neurodevelopmental and later-onset neurodegenerative diseases, including movement disorders. The tissue specificity and temporal requirements of BLTPs in disease pathogenesis remain poorly understood. This study sought to determine the age-of-onset and tissue-specific roles of VPS13A and BLTP2 in movement disorder pathogenesis using Drosophila models. Tissue-specific knockdowns of the VPS13A ortholog (Vps13) and the BLTP2 ortholog (hobbit) were generated in neurons and muscles of Drosophila. Age-dependent locomotor behavior, neurodegeneration, and synapse development and function were analyzed. Neuron-specific loss of the Vps13 ortholog caused neurodegeneration followed by age- onset movement deficits and reduced lifespan, while muscle-specific loss affected only lifespan, revealing neurodegeneration and myopathy as independent comorbidities in VPS13A disease. In contrast, neuronal loss of the BLTP2 ortholog resulted in severe early-onset locomotor defects without neurodegeneration, while muscle loss impaired synaptogenesis and neurotransmission at the neuromuscular junction (NMJ). It is concluded that VPS13A maintains neuronal survival, while BLTP2 orchestrates synaptic development. VPS13A function in muscle does not play a role in movement defects. The phenotypic specificity of BLTP function provides mechanistic insights into distinct disease trajectories for BLTP-associated movement disorders. |
| Zheng, T., Long, K., Wang, S., Rui, M. (2025). Glial-derived TNF/Eiger signaling promotes somatosensory neurite sculpting. Cell Mol Life Sci, 82(1):47 PubMed ID: 39833565
Summary: The selective elimination of inappropriate projections is essential for sculpting neural circuits during development. The class IV dendritic arborization (C4da) sensory neurons of Drosophila remodel the dendritic branches during metamorphosis. Glial cells in the central nervous system (CNS), are required for programmed axonal pruning of mushroom body (MB) γ neurons during metamorphosis in Drosophila. However, it is entirely unknown whether the glial cells are involved in controlling the neurite pruning of C4da sensory neurons. This study shows that glial deletion of Eiger (Egr), orthologous to mammalian tumor necrosis factor TNF superfamily ligand, results in dendrite remodeling deficiency of Drosophila C4da sensory neurons. Moreover, the attenuation of neuronal Wengen (Wgn) and Grindelwald (Grnd), the receptors for TNF ligands, was also examined for defects in dendrite remodeling. It was further discover that Wgn and Grnd facilitate dendrite elimination through JNK Signaling. Overall, these findings demonstrate that glial-derived Egr signal links to the neuronal receptor Wgn/Grnd, activating the JNK signaling pathway and promoting developmental neuronal remodeling. Remarkably, these findings reveal a crucial role of peripheral glia in dendritic pruning of C4da neurons. | Rabah, Y., Berwick, J. P., Sagar, N., Pasquer, L., PlaCais, P. Y., Preat, T. (2025). Astrocyte-to-neuron H(2)O(2) signalling supports long-term memory formation in Drosophila and is impaired in an Alzheimer's disease model. Nature metabolism, 7(2):321-335 PubMed ID: 39856222
Summary: Astrocytes help protect neurons from potential damage caused by reactive oxygen species (ROS). While ROS can also exert beneficial effects, it remains unknown how neuronal ROS signalling is activated during memory formation , and whether astrocytes play a role in this process. This study discovered an astrocyte-to-neuron H2O2 signalling cascade in Drosophila that is essential for long-term memory formation. Stimulation of astrocytes by acetylcholine induces an increase in intracellular calcium ions, which triggers the generation of extracellular superoxide by astrocytic NADPH oxidase. Astrocyte-secreted superoxide dismutase 3 (Sod3) converts superoxide to hydrogen peroxide H2O2, which is imported into neurons of the olfactory memory centre, the mushroom body, as revealed by in vivo , and whether astrocytes play a role in this process. This study discovered an astrocyte-to-neuron H2O2 imaging. Notably, Sod3 activity requires copper ions, which are supplied by neuronal amyloid precursor protein. This study also found that human amyloid-β peptide, implicated in Alzheimer's disease, inhibits the nAChRα7 astrocytic cholinergic receptor and impairs memory formation by preventing H2O2 synthesis. These findings may have important implications for understanding the aetiology of Alzheimer's disease. |
| Wint, R., Cleary, M. D. (2024). Transfer RNA Levels Are Tuned to Support Differentiation During Drosophila Neurogenesis. Genes, 15(12) PubMed ID: 39766869
Summary: Neural differentiation requires a multifaceted program to alter gene expression along the proliferation to the differentiation axis. While critical changes occur at the level of transcription, post-transcriptional mechanisms allow fine-tuning of protein output. This study investigated the role of tRNAs in regulating gene expression during neural differentiation in Drosophila larval brains. tRNA abundance in neural progenitor-biased and neuron-biased brains was quantified using the hydrotRNA-seq method. These tRNA data were combined with cell type-specific mRNA decay measurements and transcriptome profiles in order to model how tRNA abundance affects mRNA stability and translation efficiency. It was found that (1) tRNA abundance is largely constant between neural progenitors and neurons but significant variation exists for 10 nuclear tRNA genes and 8 corresponding anticodon groups, (2) tRNA abundance correlates with codon-mediated mRNA decay in neuroblasts and neurons, but does not completely explain the different stabilizing or destabilizing effects of certain codons, and (3) changes in tRNA levels support a shift in translation optimization from a program supporting proliferation to a program supporting differentiation. These findings reveal coordination between tRNA expression and codon usage in transcripts that regulate neural development. | Wang, Q., Miles, L., Wang, S., Noristani, H. N., Monahan Vargas, E. J., Powell, J., O'Rourke-Ibach, S. J., Li, S., Song, Y. (2024). Targeting and anchoring the mechanosensitive ion channel Piezo to facilitate its inhibition of axon regeneration. bioRxiv, PubMed ID: 39763921
Summary: Mechanical force orchestrates a myriad of cellular events including inhibition of axon regeneration, by locally activating the mechanosensitive ion channel Piezo enriched at the injured axon tip. However, the cellular mechanics underlying Piezo localization and function remains poorly characterized. The RNA repair/splicing enzyme Rtca acts upstream of Piezo to modulate its expression and transport/targeting to the plasma membrane via Rab10 GTPase, whose expression also relies on Rtca. Loss or gain of function of Rab10 promotes or impedes Drosophila sensory neuron axon regeneration, respectively. Rab10 mediates the cell surface expression of integrin β1 (Itgb1)/mys, which colocalizes and genetically interacts with Piezo, facilitating its anchorage and engagement with the microenvironment, and subsequent activation of mechanotransduction to inhibit regeneration. Importantly, loss of Rtca, Rab10 or Itgb1 promotes CNS axon regeneration after spinal cord injury or optic nerve crush in adult mice, indicating the evolutionary conservation of the machinery. |
Thursday September 10th - Cell Cycle |
| Zakerzade, R., Chang, C. H., Chatla, K., Krishnapura, A., Appiah, S. P., Zhang, J., Unckless, R. L., Blumenstiel, J. P., Bachtrog, D., Wei, K. H. (2025). Diversification and recurrent adaptation of the synaptonemal complex in Drosophila
PLoS genetics, 21(1):e1011549 PubMed ID: 39804957
Summary: The synaptonemal complex (SC) is a protein-rich structure essential for meiotic recombination and faithful chromosome segregation. Acting like a zipper to paired homologous chromosomes during early prophase I, the complex is a symmetrical structure where central elements are connected on two sides by the transverse filaments to the chromatin-anchoring lateral elements. Despite being found in most major eukaryotic taxa implying a deeply conserved evolutionary origin, several components of the complex exhibit unusually high rates of sequence turnover. This is puzzlingly exemplified by the SC of Drosophila, where the central elements and transverse filaments display no identifiable homologs outside of the genus. This study exhaustively examined the evolutionary history of the SC in Drosophila taking a comparative phylogenomic approach with high species density to circumvent obscured homology due to rapid sequence evolution. Contrasting starkly against other genes involved in meiotic chromosome pairing, SC genes show significantly elevated rates of coding evolution due to a combination of relaxed constraint and recurrent, widespread positive selection. In particular, the central element cona and transverse filament testes expression. Surprisingly, the expression of SC genes in the germline is prone to change suggesting recurrent regulatory evolution which, in many species, resulted in high testes expression even though Drosophila males are achiasmic. Overall, this study recapitulates the poor conservation of SC components, and further uncovers that the lack of conservation extends to other modalities including copy number, genomic locale, and germline regulation. Considering the elevated testes expression in many Drosophila species and the common ancestor, it is suggested that the activity of SC genes in the male germline, while still poorly understood, may be a prime target of constant evolutionary pressures driving repeated adaptations and innovations. | Shapiro, J. G., Changela, N., Jang, J. K., Joshi, J. N., McKim, K. S. (2025). Distinct checkpoint and homolog biorientation pathways regulate meiosis I in Drosophila oocytes. PLoS genetics, 21(1):e1011400 PubMed ID: 39879252
Summary: Mitosis and meiosis have two mechanisms for regulating the accuracy of chromosome segregation: error correction and the spindle assembly checkpoint (SAC). This study investigated the function of several checkpoint proteins in meiosis I of Drosophila oocytes. Increased localization of several SAC proteins was found upon depolymerization of microtubules by colchicine. However, unattached kinetochores or errors in biorientation of homologous chromosomes do not induce increased SAC protein localization. Furthermore, the metaphase I arrest does not depend on SAC genes, suggesting the APC is inhibited even if the SAC is not functional. Two SAC proteins, ROD of the ROD-ZW10-Zwilch (RZZ) complex and MPS1, are also required for the biorientation of homologous chromosomes during meiosis I, suggesting an error correction function. Both proteins aid in preventing or correcting erroneous attachments and depend on SPC105R for localization to the kinetochore. This study defined a region of SPC105R, amino acids 123-473, that is required for ROD localization and biorientation of homologous chromosomes at meiosis I. Surprisingly, ROD removal from kinetochores and movement towards spindle poles, termed "streaming," is independent of the dynein adaptor Spindly and is not linked to the stabilization of end-on attachments. Instead, meiotic RZZ streaming appears to depend on cell cycle stage and may be regulated independently of kinetochore attachment or biorientation status. We also show that Spindly is required for biorientation at meiosis I, and surprisingly, the direction of RZZ streaming. |
| Xu, Y., Chao, A., Rinaldin, M., Kickuth, A., Brugues, J., Di Talia, S. (2025). The cell cycle oscillator and spindle length set the speed of chromosome separation in Drosophila embryos. Current biology : CB, 35(3):655-664.e653 PubMed ID: 39793565
Summary: Anaphase is tightly controlled spatiotemporally to ensure proper separation of chromosomes.] The mitotic spindle, the self-organized microtubule structure driving chromosome segregation, scales in size with the available cytoplasm. Yet, the relationship between spindle size and chromosome movement remains poorly understood. This study addresses this relationship during the cleavage divisions of the Drosophila blastoderm. The speed of chromosome separation is shown to gradually decrease during the four nuclear divisions of the blastoderm. This reduction in speed is accompanied by a similar reduction in spindle length, ensuring that these two quantities are tightly linked. Using a combination of genetic and quantitative imaging approaches, two processes were found to contribute to controlling the speed at which chromosomes move in anaphase: the activity of molecular motors important for microtubule depolymerization and sliding and the cell cycle oscillator. Specifically, wthe levels of multiple kinesin-like proteins important for microtubule depolymerization, as well as kinesin-5, were found to contribute to setting the speed of chromosome separation. This observation is further supported by the scaling of poleward flux rate with the length of the spindle. Perturbations of the cell cycle oscillator using heterozygous mutants of mitotic kinases and phosphatases revealed that the duration of anaphase increases during the blastoderm cycles and is the major regulator of chromosome velocity. Thus, this work suggests a link between the biochemical rate of mitotic exit and the forces exerted by the spindle. Collectively, it is proposed that the cell cycle oscillator and spindle length set the speed of chromosome separation in anaphase. | Rombouts, J., Tavella, F., Vandervelde, A., Phong, C., Ferrell, J. E., Jr., Yang, Q., Gelens, L. (2025). Mechanistic origins of temperature scaling in the early embryonic cell cycle. Journa;, bioRxiv, PubMed ID: PubMed ID: 39763717
Summary: Temperature profoundly impacts organismal physiology and ecological dynamics, particularly affecting ectothermic species and making them especially vulnerable to climate changes. Although complex physiological processes usually involve dozens of enzymes, empirically it is found that the rates of these processes often obey the Arrhenius equation, which was originally proposed for individual chemical reactions. This study has examined the temperature scaling of the early embryonic cell cycle, with the goal of understanding why the Arrhenius equation approximately holds and why it breaks down at temperature extremes. Using experimental data from Xenopus laevis, Xenopus tropicalis, and Danio rerio, plus published data from Caenorhabditis elegans, Caenorhabditis briggsae, and Drosophila melanogaster, this study found that the apparent activation energies (E (a) values) for the early embryonic cell cycle for diverse ectotherms are all similar, 75 ∓ 7 kJ/mol, which corresponds to a Q (10) value at 20°C of 2.8 ∓ 0.2. Using computational models, this study found that the approximate Arrhenius scaling and the deviations from it at high and low temperatures can be accounted for by biphasic temperature scaling in critical individual components of the cell cycle oscillator circuit, by imbalances in the E(a) values for different partially rate-determining enzymes, or by a combination of both. Experimental studies of cycling Xenopus extracts indicate that both of these mechanisms contribute to the general scaling of temperature, and in vitro studies of individual cell cycle regulators confirm that there is in fact a substantial imbalance in their E(a) values. These findings provide mechanistic insights into the dynamic interplay between temperature and complex biochemical processes, and into why biological systems fail at extreme temperatures. |
| Wong, S. S., Monteiro, J. M., Chang, C. C., Peng, M., Mohamad, N., Steinacker, T. L., Xiao, B., Saurya, S., Wainman, A., Raff, J. W. (2025). Centrioles generate two scaffolds with distinct biophysical properties to build mitotic centrosomes. Science advances, 11(6):eadq9549 PubMed ID: 39919171
Summary: Mitotic centrosomes assemble when centrioles recruit large amounts of pericentriolar material (PCM) around themselves. The PCM comprises hundreds of proteins, and there is much debate about its physical nature. This study shows that Drosophila Spd-2 (human CEP192) fluxes out from centrioles, recruiting Polo and Aurora A kinases to catalyze the assembly of two distinct mitotic-PCM scaffolds: a Polo-dependent Cnn scaffold, and an Aurora A-dependent TACC scaffold, which exhibit solid- and liquid-like behaviors, respectively. Both scaffolds can independently recruit PCM proteins, but both are required for proper centrosome assembly, with the Cnn scaffold providing mechanical strength, and the Transforming acidic coiled-coil protein (TACC) scaffold concentrating centriole and centrosome proteins. Recruiting Spd-2 to synthetic beads injected into early embryos reconstitutes key aspects of mitotic centrosome assembly on the bead surface, and this depends on Spd-2's ability to recruit Polo and Aurora A. Thus, Spd-2 orchestrates the assembly of two scaffolds, with distinct biophysical properties, that cooperate to build mitotic somes in flies. | Kemp, J. P., Jr., Geisler, M. S., Hoover, M., Cho, C. Y., O'Farrell, P. H., Marzluff, W. F., Duronio, R. J. (2024). Cell cycle-regulated transcriptional pausing of Drosophila replication-dependent histone genes. bioRxiv, PubMed ID: 39763942
Summary: Coordinated expression of replication-dependent (RD) histones genes occurs within the Histone Locus Body (HLB) during S phase, but the molecular steps in transcription that are cell cycle regulated are unknown. This study reports that Drosophila RNA Pol II promotes HLB formation and is enriched in the HLB outside of S phase, including G1-arrested cells that do not transcribe RD histone genes. In contrast, the transcription elongation factor Spt6 is enriched in HLBs only during S phase. Proliferating cells in the wing and eye primordium express full-length histone mRNAs during S phase but express only short nascent transcripts in cells in G1 or G2 consistent with these transcripts being paused and then terminated. Full-length transcripts are produced when Cyclin E/Cdk2 is activated as cells enter S phase. Thus, activation of transcription elongation by Cyclin E/Cdk2 and not recruitment of RNA pol II to the HLB is the critical step that links histone gene expression to cell cycle progression in Drosophila. |
Tuesday, September 8th - Transcriptional Regulation |
| Zakerzade, R., Chang, C. H., Chatla, K., Krishnapura, A., Appiah, S. P., Zhang, J., Unckless, R. L., Blumenstiel, J. P., Bachtrog, D., Wei, K. H. (2025). Diversification and recurrent adaptation of the synaptonemal complex in Drosophila PLoS Genet, 21(1):e1011549 PubMed ID: 39804957
Summary: The synaptonemal complex (SC) is a protein-rich structure essential for meiotic recombination and faithful chromosome segregation. Acting like a zipper to paired homologous chromosomes during early prophase I, the complex is a symmetrical structure where central elements are connected on two sides by the transverse filaments to the chromatin-anchoring lateral elements. Despite being found in most major eukaryotic taxa implying a deeply conserved evolutionary origin, several components of the complex exhibit unusually high rates of sequence turnover. This is puzzlingly exemplified by the SC of Drosophila, where the central elements and transverse filaments display no identifiable homologs outside of the genus. This study exhaustively examined the evolutionary history of the SC in Drosophila taking a comparative phylogenomic approach with high species density to circumvent obscured homology due to rapid sequence evolution. Contrasting starkly against other genes involved in meiotic chromosome pairing, SC genes show significantly elevated rates of coding evolution due to a combination of relaxed constraint and recurrent, widespread positive selection. In particular, the central element cona and transverse filament testes expression. Surprisingly, the expression of SC genes in the germline is prone to change suggesting recurrent regulatory evolution which, in many species, resulted in high testes expression even though Drosophila males are achiasmic. Overall, this study recapitulates the poor conservation of SC components, and further uncovers that the lack of conservation extends to other modalities including copy number, genomic locale, and germline regulation. Considering the elevated testes expression in many Drosophila species and the common ancestor, it is suggested that the activity of SC genes in the male germline, while still poorly understood, may be a prime target of constant evolutionary pressures driving repeated adaptations and innovations. | Shapiro, J. G., Changela, N., Jang, J. K., Joshi, J. N., McKim, K. S. (2025). Distinct checkpoint and homolog biorientation pathways regulate meiosis I in Drosophila oocytes. PLoS genetics, 21(1):e1011400 PubMed ID: 39879252
Summary: Mitosis and meiosis have two mechanisms for regulating the accuracy of chromosome segregation: error correction and the spindle assembly checkpoint (SAC). This study investigated the function of several checkpoint proteins in meiosis I of Drosophila oocytes. Increased localization of several SAC proteins was found upon depolymerization of microtubules by colchicine. However, unattached kinetochores or errors in biorientation of homologous chromosomes do not induce increased SAC protein localization. Furthermore, the metaphase I arrest does not depend on SAC genes, suggesting the APC is inhibited even if the SAC is not functional. Two SAC proteins, ROD of the ROD-ZW10-Zwilch (RZZ) complex and MPS1, are also required for the biorientation of homologous chromosomes during meiosis I, suggesting an error correction function. Both proteins aid in preventing or correcting erroneous attachments and depend on SPC105R for localization to the kinetochore. This study defined a region of SPC105R, amino acids 123-473, that is required for ROD localization and biorientation of homologous chromosomes at meiosis I. Surprisingly, ROD removal from kinetochores and movement towards spindle poles, termed "streaming," is independent of the dynein adaptor Spindly and is not linked to the stabilization of end-on attachments. Instead, meiotic RZZ streaming appears to depend on cell cycle stage and may be regulated independently of kinetochore attachment or biorientation status. We also show that Spindly is required for biorientation at meiosis I, and surprisingly, the direction of RZZ streaming. |
| Xu, Y., Chao, A., Rinaldin, M., Kickuth, A., Brugues, J., Di Talia, S. (2025). The cell cycle oscillator and spindle length set the speed of chromosome separation in Drosophila embryos. Current biology : CB, 35(3):655-664.e653 PubMed ID: 39793565
Summary: Anaphase is tightly controlled spatiotemporally to ensure proper separation of chromosomes.] The mitotic spindle, the self-organized microtubule structure driving chromosome segregation, scales in size with the available cytoplasm. Yet, the relationship between spindle size and chromosome movement remains poorly understood. This study addresses this relationship during the cleavage divisions of the Drosophila blastoderm. The speed of chromosome separation is shown to gradually decrease during the four nuclear divisions of the blastoderm. This reduction in speed is accompanied by a similar reduction in spindle length, ensuring that these two quantities are tightly linked. Using a combination of genetic and quantitative imaging approaches, two processes were found to contribute to controlling the speed at which chromosomes move in anaphase: the activity of molecular motors important for microtubule depolymerization and sliding and the cell cycle oscillator. Specifically, wthe levels of multiple kinesin-like proteins important for microtubule depolymerization, as well as kinesin-5, were found to contribute to setting the speed of chromosome separation. This observation is further supported by the scaling of poleward flux rate with the length of the spindle. Perturbations of the cell cycle oscillator using heterozygous mutants of mitotic kinases and phosphatases revealed that the duration of anaphase increases during the blastoderm cycles and is the major regulator of chromosome velocity. Thus, this work suggests a link between the biochemical rate of mitotic exit and the forces exerted by the spindle. Collectively, it is proposed that the cell cycle oscillator and spindle length set the speed of chromosome separation in anaphase. | Rombouts, J., Tavella, F., Vandervelde, A., Phong, C., Ferrell, J. E., Jr., Yang, Q., Gelens, L. (2025). Mechanistic origins of temperature scaling in the early embryonic cell cycle. Journa;, bioRxiv, PubMed ID: PubMed ID: 39763717
Summary: Temperature profoundly impacts organismal physiology and ecological dynamics, particularly affecting ectothermic species and making them especially vulnerable to climate changes. Although complex physiological processes usually involve dozens of enzymes, empirically it is found that the rates of these processes often obey the Arrhenius equation, which was originally proposed for individual chemical reactions. This study has examined the temperature scaling of the early embryonic cell cycle, with the goal of understanding why the Arrhenius equation approximately holds and why it breaks down at temperature extremes. Using experimental data from Xenopus laevis, Xenopus tropicalis, and Danio rerio, plus published data from Caenorhabditis elegans, Caenorhabditis briggsae, and Drosophila melanogaster, this study found that the apparent activation energies (E (a) values) for the early embryonic cell cycle for diverse ectotherms are all similar, 75 ∓ 7 kJ/mol, which corresponds to a Q (10) value at 20°C of 2.8 ∓ 0.2. Using computational models, this study found that the approximate Arrhenius scaling and the deviations from it at high and low temperatures can be accounted for by biphasic temperature scaling in critical individual components of the cell cycle oscillator circuit, by imbalances in the E(a) values for different partially rate-determining enzymes, or by a combination of both. Experimental studies of cycling Xenopus extracts indicate that both of these mechanisms contribute to the general scaling of temperature, and in vitro studies of individual cell cycle regulators confirm that there is in fact a substantial imbalance in their E(a) values. These findings provide mechanistic insights into the dynamic interplay between temperature and complex biochemical processes, and into why biological systems fail at extreme temperatures. |
| Wong, S. S., Monteiro, J. M., Chang, C. C., Peng, M., Mohamad, N., Steinacker, T. L., Xiao, B., Saurya, S., Wainman, A., Raff, J. W. (2025). Centrioles generate two scaffolds with distinct biophysical properties to build mitotic centrosomes. Science advances, 11(6):eadq9549 PubMed ID: 39919171
Summary: Mitotic centrosomes assemble when centrioles recruit large amounts of pericentriolar material (PCM) around themselves. The PCM comprises hundreds of proteins, and there is much debate about its physical nature. This study shows that Drosophila Spd-2 (human CEP192) fluxes out from centrioles, recruiting Polo and A HREF="../dbzhnsky/auroraa1.htm">Aurora A kinases to catalyze the assembly of two distinct mitotic-PCM scaffolds: a Polo-dependent Cnn scaffold, and an Aurora A-dependent TACC scaffold, which exhibit solid- and liquid-like behaviors, respectively. Both scaffolds can independently recruit PCM proteins, but both are required for proper centrosome assembly, with the Cnn scaffold providing mechanical strength, and the Transforming acidic coiled-coil protein (TACC) scaffold concentrating centriole and centrosome proteins. Recruiting Spd-2 to synthetic beads injected into early embryos reconstitutes key aspects of mitotic centrosome assembly on the bead surface, and this depends on Spd-2's ability to recruit Polo and Aurora A. Thus, Spd-2 orchestrates the assembly of two scaffolds, with distinct biophysical properties, that cooperate to build mitotic somes in flies. | Kemp, J. P., Jr., Geisler, M. S., Hoover, M., Cho, C. Y., O'Farrell, P. H., Marzluff, W. F., Duronio, R. J. (2024). Cell cycle-regulated transcriptional pausing of Drosophila replication-dependent histone genes. bioRxiv, PubMed ID: 39763942
Summary: Coordinated expression of replication-dependent (RD) histones genes occurs within the Histone Locus Body (HLB) during S phase, but the molecular steps in transcription that are cell cycle regulated are unknown. This study reports that Drosophila RNA Pol II promotes HLB formation and is enriched in the HLB outside of S phase, including G1-arrested cells that do not transcribe RD histone genes. In contrast, the transcription elongation factor Spt6 is enriched in HLBs only during S phase. Proliferating cells in the wing and eye primordium express full-length histone mRNAs during S phase but express only short nascent transcripts in cells in G1 or G2 consistent with these transcripts being paused and then terminated. Full-length transcripts are produced when Cyclin E/Cdk2 is activated as cells enter S phase. Thus, activation of transcription elongation by Cyclin E/Cdk2 and not recruitment of RNA pol II to the HLB is the critical step that links histone gene expression to cell cycle progression in Drosophila. |
Tuesday, September 8th - Transcriptional Regulation |
| Fujioka, M., Ke, W., Schedl, P., Jaynes, J. B. (2025). The homie insulator has sub-elements with different insulating and long-range pairing properties. bioRxiv, PubMed ID: 39896478
Summary: Chromatin insulators are major determinants of chromosome architecture. Specific architectures induced by insulators profoundly influence nuclear processes, including how enhancers and promoters interact over long distances and between homologous chromosomes. Insulators can pair with copies of themselves in trans to facilitate homolog pairing. They can also pair with other insulators, sometimes with great specificity, inducing long-range chromosomal loops. Contrary to their canonical function of enhancer blocking, these loops can bring distant enhancers and promoters together to activate gene expression, while at the same time blocking other interactions in cis. The details of these effects depend on the choice of pairing partner, and on the orientation specificity of pairing, implicating the 3-dimensional architecture as a major functional determinant. This study dissected the homie insulator from the Drosophila even skipped (eve) locus, to understand its substructure. Pairing function were tested based on homie-carrying transgenes interacting with endogenous eve. The assay is sensitive to both pairing strength and orientation. Using this assay, a Su(Hw) binding site in homie was found to be required for efficient long-range interaction, although some activity remains without it. This binding site also contributes to the canonical insulator activities of enhancer blocking and barrier function. Based on this and other results from the functional dissection, each of the canonical insulator activities, chromosomal loop formation, enhancer blocking, and barrier activity, are partially separable. These results show the complexity inherent in insulator functions, which can be provided by an array of different proteins with both shared and distinct properties. | Wood, J. L., Nepal, S., Jones, B. W. (2025). Autoregulation of the glial gene reversed polarity in Drosophila. Scientific reports, 15(1):1238 PubMed ID: 39774987
Summary: During development, cells of the nervous system begin as unspecified precursors and proceed along one of two developmental paths to become either neurons or glia. Work in the fruit fly Drosophila melanogaster has established the role of the transcription factor Glial cells missing (Gcm) in directing neuronal precursor cells to assume a glial cell fate. Gcm acts on many target genes, one of which is reversed polarity (repo). repo encodes a homeodomain transcription factor and is necessary for the terminal differentiation of glial cells. Transient Gcm expression is followed by maintained expression of repo. Evidence supports autoregulation to be one of the mechanisms that maintains repo expression, as ectopic repo expression in embryos can activate repo-lacZ reporter constructs. This paper further explores the ability of repo to activate reporter constructs in transgenic embryos and in cultured S2 cells. Further evidence is provided that Repo protein acts as a transcription factor on its own regulatory DNA sequence. Three canonical Repo binding sites (RBSs) are located within the upstream 4.3 kilobase repo cis-regulatory DNA (CRD). The upstream 2 kb within the repo CRD has remarkable repo-dependent gene expression activity, and mutagenesis of RBS1 in this 2 kb region results in a significant decrease in repo-induced reporter gene expression in both systems. These results in cell culture experiments also show that RBS2 and/or RBS3 can affect repo-dependent gene expression in the context of the whole upstream repo CRD. Mutagenesis of both RBS2 and RBS3 in the repo CRD, leaving RBS1 intact, significantly reduces repo-induced reporter gene expression. These results suggest that all three canonical RBSs may be cooperatively involved in autoregulation of repo expression. |
| Kudryashova, K. S., Deriglazova, I. O., Osadchiy, I. S., Georgiev, P., Maksimenko, O. (2024). Construction of Promoter Elements for Strong, Moderate, and Weak Gene Expression in Drosophila melanogaster. Genes, 16(1) PubMed ID: 39858550
Summary: Transcriptional promoters play an essential role in regulating protein expression. Promoters with weak activity generally lead to low levels of expression, resulting in fewer proteins being produced. At the same time, strong promoters are commonly used in studies using transgenic organisms as model systems. This approach can have various negative consequences for the organism, as many regulatory proteins need to be expressed in small quantities, and excessive expression can have harmful effects on cells and organisms. Therefore, it is important to select the right promoter when creating transgenic organisms for research and practical applications. In this study, the Drosophila melanogaster genome was used as a source of natural promoter sequences for RNA polymerase II. These sequences were extracted and used to create a set of promoters that are suitable for practical application. The promoters were tested in a model system using fluorescent reporter genes in S2 cells and transgenic lines of Drosophila. This study assessed the expression levels of fluorescent reporter genes to rank the tested promoters from strongest to weakest. Six individual promoters of different sizes were established and compared. Additionally, three pairs of bidirectional promoters were designed and tested that could be used to simultaneously express two proteins. Based on these findings, the tested promoters were grouped into three categories: strong, moderate, and weak. These promoters can be utilized in transgenic model systems for protein production at different levels, from high to low. Bidirectional promoters, constructed "head-to-head", meaning oppositely directed with the minimum distance between them, represent a novel tool for the co-expression of proteins. | Pimmett, V. L., McGehee, J., Trullo, A., Douaihy, M., Radulescu, O., Stathopoulos, A., Lagha, M. (2025). Optogenetic manipulation of nuclear Dorsal reveals temporal requirements and consequences for transcription. Development, 152(6) PubMed ID: 40018801
Summary: Morphogen gradients convey essential spatial information during tissue patterning. Although the concentration and timing of morphogen exposure are both crucial, how cells interpret these graded inputs remains challenging to address. This study employed an optogenetic system to acutely and reversibly modulate the nuclear concentration of the morphogen Dorsal (DL), homolog of NF-kappaB, which orchestrates dorsoventral patterning in the Drosophila embryo. By controlling DL nuclear concentration while simultaneously recording target gene outputs in real time, this study identified a critical window for DL action that is required to instruct patterning and characterized the resulting effect on spatiotemporal transcription of target genes in terms of timing, coordination and bursting. A transient decrease was found in nuclear DL levels at nuclear cycle 13 leads to reduced expression of the mesoderm-associated gene snail (sna) and partial derepression of the neurogenic ectoderm-associated target short gastrulation (sog) in ventral regions. Surprisingly, the mispatterning elicited by this transient change in DL was detectable at the level of single-cell transcriptional bursting kinetics, specifically affecting long inter-burst durations. This approach of using temporally resolved and reversible modulation of a morphogen in vivo, combined with mathematical modeling, establishes a framework for understanding the stimulus-response relationships that govern embryonic patterning. |
| Mukherjee, A., Kapoor, M., Shankta, K., Fallacaro, S., Carter, R. D., Ratchasanmuang, P., Haloush, Y. I., Mir, M. (2025). A cluster of RNA Polymerase II molecules is stably associated with an active gene. bioRxiv, PubMed ID: 39990393
Summary: In eukaryotic nuclei, transcription is associated with discrete foci of RNA Polymerase II (RNAPII) molecules. How these clusters interact with genes and their impact on transcriptional activity remain heavily debated. This study took advantage of the naturally occurring increase in transcriptional activity during Zygotic Genome Activation (ZGA) in Drosophila melanogaster embryos to characterize the functional roles of RNAPII clusters in a developmental context. Using single-molecule tracking and lattice light-sheet microscopy, this study found that RNAPII cluster formation depends on transcription initiation and that cluster lifetimes are reduced upon transcription elongation. Single clusters are stably associated with active gene loci during transcription and that cluster intensities are strongly correlated with transcriptional output. These data suggest that prior to ZGA, RNAPII clusters prime genes for activation, whereas after ZGA, clusters are composed mostly of elongating molecules at individual genes. | Soldatova, I. V., Shepelev, M. V., Georgiev, P., Tikhonov, M. (2024). A Novel Mechanism for Transcription Termination in the mod(mdg4) Locus of Drosophila melanogaster. Biology, 13(12) PubMed ID: 39765661
Summary: This study investigated an alternative mechanism of transcription termination that occurs independently of polyadenylation. We focused on a non-canonical transcription terminator (NTT) identified in the mod(mdg4) gene of Drosophila melanogaster. Using a developed model system, we demonstrated that the minimal functional unit of the NTT consists of 79 nucleotides that form a specific secondary RNA structure. Our results indicate that transcripts generated from the NTT exhibit reduced stability and are hindered in their export to the cytoplasm. An NTT from the distantly related species D. willistoni could function as a transcription terminator in D. melanogaster cells, highlighting the importance of conserved motifs for NTT functionality. At the same time, the NTT did not function in human cells, suggesting that the interaction of the NTT with specific protein factors is required to terminate transcription. |
Friday, September 4th - Embryonic Development |
| O'Leary, T. S., Mikucki, E. E., Tangwancharoen, S., Boyd, J. R., Frietze, S., Helms Cahan, S., Lockwood, B. L. (2025). Single-nuclei multiome ATAC and RNA sequencing reveals the molecular basis of thermal plasticity in Drosophila melanogaster embryos. bioRxiv, PubMed ID: 39829925
Summary: Embryogenesis is remarkably robust to temperature variability, yet there is limited understanding of the homeostatic mechanisms that offset thermal effects during early development. This study measured the thermal acclimation response of upper thermal limits and profiled chromatin state and the transcriptome of D. melanogaster embryos (Bownes Stage 11) using single-nuclei multiome ATAC and RNA sequencing. Thermal acclimation, while preserving a common set of primordial cell types, rapidly shifted the upper thermal limit. Cool-acclimated embryos showed a homeostatic response characterized by increased chromatin accessibility at transcription factor binding motifs for the transcriptional activator Zelda, along with enhanced activity of gene regulatory networks in the primordial cell types including the foregut and hindgut, mesoderm, and peripheral nervous system. In addition, cool-acclimated embryos had higher expression of genes encoding ribosomal proteins and enzymes involved in oxidative phosphorylation. Despite the hypothesis that differential heat tolerance might be explained by differential expression of molecular chaperones, widespread differences in the chromatin accessibility or expression of heat shock genes were not observed. Overall, these results suggest that environmental robustness to temperature during embryogenesis necessitates homeostatic gene expression responses that regulate the speed of development, potentially imposing metabolic costs that constrain upper thermal limits. | Reyes, R., Rodriguez-MuNoz, R., Nahmad, M. (2025). Cell recruitment and the origins of Anterior-Posterior asymmetries in the Drosophila wing. PloS one, 20(1):e0313067 PubMed ID: 39752433
Summary: The mechanisms underlying the establishment of asymmetric structures during development remain elusive. The wing of Drosophila is asymmetric along the Anterior-Posterior (AP) axis, but the developmental origins of this asymmetry is unknown. This study investigated the contribution of cell recruitment, a process that drives cell fate differentiation in the Drosophila wing disc, to the asymmetric shape and pattern of the adult wing. Genetic impairment of cell recruitment in the wing disc results in a significant gain of AP symmetry, which results from a reduction of the region between longitudinal vein 5 and the wing margin (L5-M) in the adult wing. Morphometric analysis confirms that blocking of cell recruitment results in a more symmetric wing with respect to controls, suggesting a contribution of cell recruitment to the establishment of asymmetry in the adult wing. In order to verify if this phenotype is originated during the time in which cell recruitment occurs during larval development, this study examined the expression of a reporter for the selector gene vestigial (vg) in the corresponding pro-vein regions of the wing disc, but these findings could not explain the findings in adult wings. However, the circularity of the Vg pattern significantly increases in recruitment-impaired wing discs, suggesting that cell recruitment may contribute to AP asymmetries in the adult wing shape by altering the roundness of the Vg pattern. It is concluded that cell recruitment, a widespread mechanism that participates in growth and patterning of several developing systems, may contribute, at least partially, to the asymmetric shape of the Drosophila wing. |
| Richa, P., Haring, M., Wang, Q., Choudhury, A. R., Gopfert, M. C., Wolf, F., Grosshans, J., Kong, D. (2025). Synchronization in epithelial tissue morphogenesis. Curr Biol, 35(11):2495-2508.e2494 PubMed ID: 40239658
Summary: Coordination of cell behavior is central to morphogenesis, when arrays of cells simultaneously undergo shape changes or dynamic rearrangements. In epithelia, cell shape changes invariably exert mechanical forces, which adjacent cells could sense to trigger an active response. However, molecular mechanisms for such mechano-transduction and especially their role for tissue-wide coordination in morphogenesis have remained ambiguous. This study investigated the function of Tmc, a key component of cellular mechano-transduction in vertebrate hearing, for coordination of cell dynamics in the epithelial amnioserosa of Drosophila embryos. Cell-cell mechano-transduction was directly probed in vivo by opto-chemically inducing single-cell contractions and discovered a Tmc-dependent contraction response in neighboring cell groups. On the tissue scale; synchronization was discovered of neighboring cell area oscillations, which is impaired in Tmc mutants. A data-driven model of Tmc-dependent cell-cell interactions predicts that synchronization leads to an isotropic force map and effectively shields the tissue from external mechanical pulling. By microdissection, equal junction tension was observed along the axial and lateral axis in wild-type but increased lateral tension in Tmc mutants. Thus, Tmc transduces forces into an intracellular response that coordinates mechanical cell behavior in epithelial tissue. | Linvill, K., Russell, L. J., Vanderleest, T. E., Miao, H., Xie, Y., Blankenship, J. T., Loerke, D. (2025). Rectification of planar orientation angle switches behavior and replenishes contractile junctions. The Journal of cell biology, 224(4) PubMed ID: 39846952
Summary: In the early Drosophila embryo, germband elongation is driven by oriented cell intercalation through t1 transitions, where vertical (dorsal-ventral aligned) interfaces contract and then resolve into new horizontal (anterior-posterior aligned) interfaces. Contractile events produce a continuous "rectification" of cell interfaces, in which interfaces systematically rotate toward more vertical orientations. As interfaces rotate, their behavior transitions from elongating to contractile regimes, indicating that the planar polarized identities of cell-cell interfaces are continuously re-interpreted in time depending on their orientation angle. Rotating interfaces acquire higher levels of Myosin II motor proteins as they become more vertical, while disruptions to the contractile molecular machinery reduce the rates of rotation. Through this angle rectification, the available pool of contractile interfaces is continuously replenished, as new interfaces acquire a contractile identity through rotation. Thus, individual cells acquire additional interfaces that are capable of undergoing t1 transitions, allowing cells to participate in multiple staggered rounds of intercalation events. |
| Tah, I., Haertter, D., Crawford, J. M., Kiehart, D. P., Schmidt, C. F., Liu, A. J. (2025). A minimal vertex model explains how the amnioserosa avoids fluidization during Drosophila dorsal closure. Journal Proceedings of the National Academy of Sciences 122(1):e2322732121 PubMed ID: 39793057
Summary: Dorsal closure is a process that occurs during embryogenesis of Drosophila melanogaster. During dorsal closure, the amnioserosa (AS), a one-cell thick epithelial tissue that fills the dorsal opening, shrinks as the lateral epidermis sheets converge and eventually merge. During this process, both shape index and aspect ratio of amnioserosa cells increase markedly. The standard 2-dimensional vertex model, which successfully describes tissue sheet mechanics in multiple contexts, would in this case predict that the tissue should fluidize via cell neighbor changes. Surprisingly, however, the amnioserosa remains an elastic solid with no such events. This study presents a minimal extension to the vertex model that explains how the amnioserosa can achieve this unexpected behavior. Continuous shrinkage of the preferred cell perimeter and cell perimeter polydispersity lead to the retention of the solid state of the amnioserosa. This model accurately captures measured cell shape and orientation changes and predicts nonmonotonic junction tension that we confirm with laser ablation experiments. | Sokolowski, T. R., Gregor, T., Bialek, W., Tkacik, G. (2025). Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences 122(1):e2402925121 PubMed ID: 39752518
Summary: >Many biological systems operate near the physical limits to their performance, suggesting that aspects of their behavior and underlying mechanisms could be derived from optimization principles. However, such principles have often been applied only in simplified models. This study explores a detailed mechanistic model of the gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize the information that gene expression levels provide about nuclear positions. This optimization is conducted under realistic constraints, such as limits on the number of available molecules. Remarkably, the optimal networks derived closely match the architecture and spatial gene expression profiles observed in the real organism. This framework quantifies the tradeoffs involved in maximizing functional performance and allows for the exploration of alternative network configurations, addressing the question of which features are necessary and which are contingent. Our results suggest that multiple solutions to the optimization problem might exist across closely related organisms, offering insights into the evolution of gene regulatory networks. |
Thursday, September 3rd - Disease Models |
| Langhammer, F., Gregor, A., Ntamati, N. R., Ekici, A. B., Winner, B., Nevian, T., Zweier, C. (2025). Deregulated ion channels contribute to RHOBTB2-associated developmental and epileptic encephalopathy.
Human molecular genetics, 34(7):639-650 PubMed ID: 39849855
Summary: While de novo missense variants in the BTB domains of atypical RhoGTPase RHOBTB2 cause a severe developmental and epileptic encephalopathy, de novo missense variants in the GTPase domain or bi-allelic truncating variants are associated with more variable neurodevelopmental and seizure phenotypes. Apart from the observation of RHOBTB2 abundance resulting from BTB-domain variants and increased seizure susceptibility in Drosophila overexpressing RhoBTB, knowledge on RHOBTB2-related pathomechanisms is limited. This study now found enrichment for ion channels among the differentially expressed genes from RNA-Seq on fly heads overexpressing RhoBTB. Subsequent genetic interaction experiments confirmed a functional link between RhoBTB and paralytic, the orthologue of human sodium channels, including epilepsy associated SCN1A, in vivo. Patch-clamp recordings were performed on mature neurons differentiated from human induced pluripotent stem cells with either homozygous frameshifts or patient-specific heterozygous missense variants in the GTPase or the BTB domains. This revealed significantly altered neuronal activity and excitability resulting from BTB domain variants but not from GTPase domain variants or upon complete loss of RHOBTB2. This study indicates a role of deregulated ion channels in the pathogenesis of RHOBTB2-related developmental and epileptic encephalopathy and points to specific pathomechanisms underlying the observed genotype-phenotype correlations regarding variant zygosity, location and nature. | Lai, Y., Reina-Gonzalez, P., Maor, G., Miller, G. W., Sarkar, S. (2025). Biotin mitigates the development of manganese-induced, Parkinson's disease-related neurotoxicity in Drosophila and human neurons.
Science signaling, 18(870):eadn9868 PubMed ID: 39836750
Summary: Chronic exposure to manganese (Mn) induces manganism and has been widely implicated as a contributing environmental factor to Parkinson's disease (PD), featuring notable overlaps between the two in motor symptoms and clinical hallmarks. This study developed an adult Drosophila model of Mn toxicity that recapitulated key parkinsonian features, spanning behavioral deficits, neuronal loss, and dysfunctions in lysosomes and mitochondria. Metabolomics analysis of the brain and body tissues of these flies at an early stage of toxicity identified systemic changes in the metabolism of biotin (also known as vitamin B(7)) in Mn-treated groups. Biotinidase-deficient flies showed exacerbated Mn-induced neurotoxicity, parkinsonism, and mitochondrial dysfunction. Supplementing the diet of wild-type flies with biotin ameliorated the pathological phenotypes of concurrent exposure to Mn. Biotin supplementation also ameliorated the pathological phenotypes of three standard fly models of PD. Furthermore, supplementing the culture media of human induced stem cells (iPSCs) differentiated midbrain dopaminergic neurons with biotin protected against Mn-induced mitochondrial dysregulation, cytotoxicity, and neuronal loss. Last, analysis of the expression of genes encoding biotin-related proteins in patients with PD revealed increased amounts of biotin transporters in the substantia nigra compared with healthy controls, suggesting a potential role of altered biotin metabolism in PD. Together, these findings identified changes in biotin metabolism as underlying Mn neurotoxicity and parkinsonian pathology in flies, for which dietary biotin supplementation was preventative. |
| Sun, Z., Li, L., Zhang, L. (2025). Apigenin enhancing oxidative resistance and proteostasis to extend lifespan via PTEN-mediated AKT signalling pathway. Biochim Biophys Acta Mol Basis Dis, 1871(3):167670 PubMed ID: 39826849
Summary: Aging is a complicated process, featuring the progressive deterioration of physiological functions and a heightened susceptibility to diseases including neurodegenerative disorders, cardiovascular diseases, and cancer. Apigeninoxidative stress in both organisms, as manifested by enhanced survival, decreased reactive oxygen species (ROS) levels and upregulation of antioxidant enzymes. Furthermore, apigenin activates crucial elements of the proteostasis network (PN), such as upregulation of proteostasis-related enzymes activity and genes expression. Network analysis revealed that apigenin affects aging conserved in the longevity-regulating pathway. Notably, Pten is a hub target in flies. Apigenin regulated DmPten at both mRNA and protein expression level while modulating downstream targets, including the phosphorylation of AKT and associated signalling pathways. In a high-sucrose diet (HSD) model, Apigenin treatment extended lifespan, reduced hemolymph glucose levels, enhanced Pten expression, suppressed AKT phosphorylation, and modulated the phosphorylation status of S6K and expression of DmFoxo. These results demonstrate that apigenin could serve as a longevity research object and potential therapeutic drug for promoting health and longevity through its antioxidant and proteostatic properties. | Singh, A., Hu, Y., Lopes, R. F., Lane, L., Woldemichael, H., Xu, C., Udeshi, N. D., Carr, S. A., Perrimon, N. (2025). Cell-death induced immune response and coagulopathy promote cachexia in Drosophila.
bioRxiv, PubMed ID: 39829769
Summary: Tumors can exert a far-reaching influence on the body, triggering systemic responses that contribute to debilitating conditions like cancer cachexia. To characterize the mechanisms underlying tumor-host interactions, this study utilized a BioID-based proximity labeling method to identify proteins secreted by Ykiact adult Drosophila gut tumors into the bloodstream/hemolymph. Among the major proteins identified are coagulation and immune-responsive factors that contribute to the systemic wasting phenotypes associated with Ykiact tumors. The effect of innate immunity factors is mediated by NFkappaB transcription factors Relish, Dorsal, and Dif, which in turn upregulate the expression of the cachectic factors Pvf1, Impl2, and Upd3. In addition, Ykiact tumors secrete Eiger, a TNF-alpha homolog, which activates the JNK signaling pathway in neighboring non-tumor cells, leading to cell death. The release of damage-associated molecular patterns (DAMPs) from these dying cells presumably amplifies the inflammatory response, exacerbating systemic wasting. Targeting the inflammatory response, the JNK pathway, or the production of cachectic factors could potentially alleviate the debilitating effects of cancer cachexia. |
| Oh, J., Catherine, C., Kim, E. S., Min, K. W., Jeong, H. C., Kim, H., Kim, M., Ahn, S. H., Lukianenko, N., Jo, M. G., Bak, H. S., Lim, S., Kim, Y. K., Kim, H. M., Lee, S. B., Cho, H. (2025). Engineering a membrane protein chaperone to ameliorate the proteotoxicity of mutant huntingtin.
Nature communications, 16(1):737 PubMed ID: 39824813
Summary: Toxic protein aggregates are associated with various neurodegenerative diseases, including Huntington's disease (HD). Since no current treatment delays the progression of HD, this study developed a mechanistic approach to prevent mutant huntingtin (mHttex1) aggregation. This study engineer the ATP-independent cytosolic chaperone PEX19, which targets peroxisomal membrane proteins to peroxisomes, to remove mHttex1 aggregates. Using yeast toxicity-based screening with a random mutant library, two yeast PEX19 variants were identified, and equivalent mutations were engineered into human PEX19 (hsPEX19). These variants effectively delay mHttex1 aggregation in vitro and in cellular HD models. The mutated hydrophobic residue in the α4 helix of hsPEX19 variants binds to the N17 domain of mHttex1, thereby inhibiting the initial aggregation process. Overexpression of the hsPEX19-FV variant rescues HD-associated phenotypes in primary striatal neurons and in Drosophila. Overall, these data reveal that engineering ATP-independent membrane protein chaperones is a promising therapeutic approach for rational targeting of mHttex1 aggregation in HD. | Yu, Z., Yan, J., Liu, Z., Wang, H., Luo, G., Chen, H. (2025). The Batten disease gene Cln3 is required for the activation of intestinal stem cell during regeneration via JAK/STAT signaling in Drosophila. Frontiers in cell and developmental biology, 13:1508714 PubMed ID: 39917569
Summary: CLN3 mutation causes Juvenile neuronal ceroid lipofuscinosis (JNCL, also known as Batten disease), an early onset neurodegenerative disorder. Patients who suffer from Batten disease often die at an early age. However, the mechanisms underlying how CLN3 loss develops Batten disease remain largely unclear. Using Drosophila midgut system, this study demonstrated that Drosophila Cln3 has no effect on midgut homeostasis maintaince, including cellular component, intestinal stem cells (ISCs) proliferation and differentiation, but is necessary for ISC activation upon tissue damage. Cell type-specific Gal4 screening reveals that the failure of ISC activation during regeneration caused by Cln3 loss is ISC-autonomous. Through genetic analyses, JAK/STAT signaling in ISCs is not activated with Cln3 depletion upon tissue damage, and functions downstream of Cln3. These study provides a potential mechanism underlying the development of CLN3-mediated Batten disease at cellular level. |
Wednesday, September 2nd - RNAs |
| Santos-Cruz, L. F., Campos-Aguilar, M., Castaneda-Partida, L., Sigrist-Flores, S. C., Heres-Pulido, M. E., Duenas-Garcia, I. E., Piedra-Ibarra, E., Jimenez-Flores, R., Ponciano-Gomez, A. (2025). Impact of Larval Sertraline Exposure on Alternative Splicing in Neural Tissue of Adult Drosophila melanogaster. International journal of molecular sciences, 26(2) PubMed ID: 39859278
Summary: Sertraline, a selective serotonin reuptake inhibitor (SSRI), is commonly used to treat various psychiatric disorders such as depression and anxiety due to its ability to increase serotonin availability in the brain. Recent findings suggest that sertraline may also influence the expression of genes related to synaptic plasticity and neuronal signaling pathways. Alternative splicing, a process that allows a single gene to produce multiple protein isoforms, plays a crucial role in the regulation of neuronal functions and plasticity. Dysregulation of alternative splicing events has been linked to various neurodevelopmental and neurodegenerative diseases. This study aims to explore the effects of sertraline on alternative splicing events, including exon inclusion, exon exclusion, and mutually exclusive splicing events, in genes associated with neuronal function in Drosophila melanogaster and to use this model to investigate the molecular impacts of SSRIs on gene regulation in the nervous system. RNA sequencing (RNA-seq) was performed on central nervous system samples from Drosophila melanogaster adults exposed to sertraline for 24 h when they were third instar larvae. Alternative splicing events were analyzed to identify changes in exon inclusion and exclusion, as well as intron retention. Sertraline treatment significantly altered alternative splicing patterns in key genes related to neuronal stability and function. Specifically, sertraline promoted the inclusion of long Ank2 isoforms, suggesting enhanced axonal stability, and favored long ATPalpha isoforms, which support Na(+)/K(+) ATPase activity essential for ionic balance and neuronal excitability. Intron retention in the yuri gene suggests that cytoskeletal reorganization could impact neuronal morphology. Additionally, splicing alterations in sxc and Atg18a indicate a potential influence of sertraline on epigenetic regulation and autophagy processes, fundamental aspects for neuronal plasticity and cellular homeostasis. These findings suggest that sertraline influences alternative splicing in the central nervous system of Drosophila melanogaster, potentially contributing to its therapeutic effects by modulating neuronal stability and adaptability. | Parikh, R. Y., Nayak, D., Lin, H., Gangaraju, V. K. (2025). Drosophila Modulo is essential for transposon silencing and developmental robustness. The Journal of biological chemistry, 301(3):108210 PubMed ID: 39848495
Summary: Transposable element (TE) silencing in the germline is crucial for preserving genome integrity; its absence results in sterility and diminished developmental robustness. The Piwi-interacting RNA (piRNA) pathway is the primary small non-coding RNA mechanism by which TEs are silenced in the germline. Three piRNA binding proteins promote the piRNA pathway function in the germline- P-element-induced wimpy testis (Piwi), Aubergine (Aub), and Argonaute 3 (Ago3). Piwi mediates transcriptional silencing of TEs by promoting the deposition of the heterochromatin mark Histone 3 lysine nine trimethylation (H3K9me3) at TE genomic sites. Aub and Ago3 facilitate post-transcriptional silencing of TEs. Proteins and mechanisms that promote piRNA function in TE silencing are still being discovered. This study demonstrates that the Drosophila Modulo protein, a homolog of mammalian Nucleolin and an epigenetic regulator, is crucial for the enrichment of H3K9me3 at TEs. We show that Modulo interacts with Piwi and operates downstream of the Piwi-piRNA complex's entry into the nucleus. Lack of Modulo function impairs Piwi-interacting protein Panoramix's ability to target transposon RNAs. Furthermore, the reduced function of Modulo in the mother undermines developmental robustness and exacerbates neomorphic a specific dominant, gain-of-function mutant allele of the Kruppel, Kr[If-1], induced ectopic eye outgrowths in the offspring. Maternal Modulo enhances developmental robustness by inhibiting TE activation and transcriptome variability associated with intrinsic genetic variation. Thus, Modulo is an essential component of the mechanism that operates in the maternal germline to facilitate TE silencing and ensure developmental robustness in the ensuing generation. |
| Scarpa, A., Pianezza, R., Gellert, H. R., Haider, A., Kim, B. Y., Lai, E. C., Kofler, R., Signor, S. (2025). Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years. Nature communications, 16(1):516 PubMed ID: 39788974
Summary: Horizontal transfer of genetic material in eukaryotes has rarely been documented over short evolutionary timescales. This study shows that two retrotransposons, Shellder and Spoink, invaded the genomes of multiple species of the melanogaster subgroup within the last 50 years. Through horizontal transfer, Spoink spread in D. melanogaster during the 1980s, while both Shellder and Spoink invaded D. simulans in the 1990s. Possibly following hybridization, D. simulans infected the island endemic species D. mauritiana (Mauritius) and D. sechellia (Seychelles) with both TEs after 1995. In the same approximate time-frame, Shellder also invaded D. teissieri, a species confined to sub-Saharan Africa. The donors of Shellder and Spoink are likely American Drosophila species from the willistoni, cardini, and repleta groups. Thus, the described cascade of TE invasions could only become feasible after D. melanogaster and D. simulans extended their distributions into the Americas 200 years ago, likely aided by human activity. This work reveals that cascades of TE invasions, likely initiated by human-mediated range expansions, could have an impact on the genomic and phenotypic evolution of geographically dispersed species. Within a few decades, TEs could invade many species, including island endemics, with distributions very distant from the donor of the TE. | Liu, M., Xie, X. J., Li, X., Ren, X., Sun, J. L., Lin, Z., Hemba-Waduge, R. U., Ji, J. Y. (2025). Transcriptional coupling of telomeric retrotransposons with the cell cycle.. Science advances, 11(1):eadr2299 PubMed ID: 39752503
Summary: Unlike most species that use telomerase for telomere maintenance, many dipterans, including Drosophila, rely on three telomere-specific retrotransposons (TRs)-HeT-A, TART, and TAHRE-to form tandem repeats at chromosome ends. Although TR transcription is crucial in their life cycle, its regulation remains poorly understood. This study identifies the Mediator complex, E2F1-Dp, and Scalloped/dTEAD as key regulators of TR transcription. Reducing the activity of the Mediator or Sd/dTEAD increases TR expression and telomere length, while overexpressing E2F1-Dp or depleting Rbf1 stimulates TR transcription. The Mediator and Sd/dTEAD regulate this process through E2F1-Dp. CUT&RUN (Cleavage under targets and release using nuclease) analysis shows direct binding of CDK8, Dp, and Sd/dTEAD to telomeric repeats, with motif enrichment revealing E2F- and TEAD-binding sites. These findings uncover the Mediator complex's role in controlling TR transcription and telomere length through E2F1-Dp and Sd, coupling the transcriptional regulation of the TR life cycle with host cell-cycle machinery to protect chromosome ends in Drosophila. |
| Li, M., Yu, X., Yao, Z., Gao, X., Liu, Q., Zhou, Z., Zhao, Y. (2025). Targeting the Hh and Hippo pathways by miR-7 suppresses the development of insect wings. Insect science, PubMed ID: 39823176
Summary: Wings are important organs of insects involved in flight, mating, and other behaviors, and are therefore prime targets for pest control. The formation of insect wings is a complex process that is regulated by multiple pathways. The Hedgehog (Hh) pathway regulates the distribution of wing veins, while the Hippo pathway modulates wing size. Any interventions that can manipulate these pathways have the potential to disrupt wing development and could be used for pest control. This study found that overexpression of miR-7 in Drosophila results in smaller wings with disordered veins. Mechanistically, miR-7 directly targets both ci and yki via different mature miRNAs (miR-7-5p and miR-7-3p), thereby disrupting the Hh and Hippo pathways. Importantly, this regulatory mechanism is also observed in another insect species, Helicoverpa armigera. Finally, by utilizing a nanocarrier delivery system, this study showed that introducing miR-7 via star polycation (SPc), a star-shaped, positively charged nanomaterial used as a carrier for delivering genetic material, leads to wing defects in H. armigera. In conclusion, these findings uncover that miR-7 inhibits wing formation by targeting both the Hippo and Hh pathways, indicating its potential for use in pest control strategies. | Li, J., Xu, S., Liu, Z., Yang, L., Ming, Z., Zhang, R., Zhao, W., Peng, H., Quinn, J. J., Wu, M., Geng, Y., Zhang, Y., He, J., Chen, M., Li, N., Shao, N. Y., Ma, Q. (2025). A noncanonical role of roX RNAs in autosomal epigenetic repression. Nature communications, 16(1):155 PubMed ID: 39747148
Summary: Long noncoding RNAs known as roX (RNA on the X) are crucial for male development in Drosophila, as their loss leads to male lethality from the late larval stages. While roX RNAs are recognized for their role in sex-chromosome dosage compensation, ensuring balanced expression of X-linked genes in both sexes, their potential influence on autosomal gene regulation remains unexplored. Using an integrative multi-omics approach, this study showed that roX RNAs not only govern the X chromosome but also target genes on autosomes that lack male-specific lethal (MSL) complex occupancy, together with Polycomb repressive complexes (PRCs). This study observed that roX RNAs colocalize with MSL proteins on the X chromosome and PRC components on autosomes. Intriguingly, loss of roX function reduces X-chromosomal H4K16ac levels and autosomal H3K27me3 levels. Correspondingly, X-linked genes display reduced expression, whereas many autosomal genes exhibit elevated expression upon roX loss. These findings propose a dual role for roX RNAs: activators of X-linked genes and repressors of autosomal genes, achieved through interactions with MSL and PRC complexes, respectively. This study uncovers the unconventional epigenetic repressive function of roX RNAs with PRC interaction. |
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