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| ARCHIVE | Saturday, March 9th - Cell Cycle |
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December 2024 January 2025 November 2024 October 2024 September 2024 August 2024 July 2024 June 2024 May 2024 April 2024 March 2024 February 2024 January 2024 December 2023 November 2023 October 2023 September 2023 August 2023 July 2023 June 2023 May 2023 April 2023 March 2023 February 2023 January 2023 December 2022 December 2021 December 2020 December 2019 December 2018 | Haseeb, M. A., Bernys, A. C., Dickert, E. E., Bickel, S. E. (2024). An RNAi screen to identify proteins required for cohesion rejuvenation during meiotic prophase in Drosophila oocytes. G3 (Bethesda), 14(8) PubMed ID: 38849129
Summary: Accurate chromosome segregation during meiosis requires the maintenance of sister chromatid cohesion, initially established during premeiotic S phase. In human oocytes, DNA replication and cohesion establishment occur decades before chromosome segregation and deterioration of meiotic cohesion is one factor that leads to increased segregation errors as women age. Previous work has led to a proposal that a cohesion rejuvenation program operates to establish new cohesive linkages during meiotic prophase in Drosophila oocytes and depends on the cohesin loader Nipped-B and the cohesion establishment factor Eco. In support of this model, recent work has demonstrated that chromosome-associated cohesin turns over extensively during meiotic prophase and failure to load cohesin onto chromosomes after premeiotic S phase results in arm cohesion defects in Drosophila oocytes. To identify proteins required for prophase cohesion rejuvenation but not S phase establishment, a Gal4-UAS inducible RNAi screen was conducted that utilized two distinct germline drivers. Using this strategy, 29 gene products were identifed for which hairpin expression during meiotic prophase, but not premeiotic S phase, significantly increased segregation errors. Prophase knockdown of Brahma or Pumilio, two positives with functional links to the cohesin loader, caused a significant elevation in the missegregation of recombinant homologs, a phenotype consistent with premature loss of arm cohesion. Moreover, fluorescence in situ hybridization confirmed that Brahma, Pumilio, and Nipped-B are required during meiotic prophase for the maintenance of arm cohesion. These data support the model that Brahma and Pumilio regulate Nipped-B-dependent cohesin loading during rejuvenation. Future analyses will better define the mechanism(s) that govern meiotic cohesion rejuvenation and whether additional prophase-specific positives function in this process. | Vicars, H., Karg, T., Mills, A., Sullivan, W. (2024). Acentric chromosome congression and alignment on the metaphase plate via kinetochore-independent forces in Drosophila.. bioRxiv, PubMed ID: 38798431
Summary: Chromosome congression and alignment on the metaphase plate involves lateral and microtubule plus-end interactions with the kinetochore. Here we take advantage of our ability to efficiently generate a GFP-marked acentric X chromosome fragment in Drosophila neuroblasts to identify forces acting on chromosome arms that drive congression and alignment. We find acentrics efficiently align on the metaphase plate, often more rapidly than kinetochore-bearing chromosomes. Unlike intact chromosomes, the paired sister acentrics oscillate as they move to and reside on the metaphase plate in a plane distinct and significantly further from the main mass of intact chromosomes. Consequently, at anaphase onset acentrics are oriented either parallel or perpendicular to the spindle. Parallel-oriented sisters separate by sliding while those oriented perpendicularly separate via unzipping. This oscillation, together with the fact that in monopolar spindles acentrics are rapidly shunted away from the poles, indicates that distributed plus-end directed forces are primarily responsible for acentric migration. This conclusion is supported by the observation that reduction of EB1 preferentially disrupts acentric alignment. In addition, reduction of http://Klp3a activity, a gene required for the establishment of pole-to-pole microtubules, preferentially disrupts acentric alignment. Taken together these studies suggest that plus-end forces mediated by the outer pole-to-pole microtubules are primarily responsible for acentric metaphase alignment. Surprisingly, this study found that a small fraction of sister acentrics are anti-parallel aligned indicating that the kinetochore is required to ensure parallel alignment of sister chromatids. Finally, induction of acentric chromosome fragments was found to result in a global reorganization of the congressed chromosomes into a torus configuration. |
| Marshall, W. F., Fung, J. C. (2024). Modeling homologous chromosome recognition via nonspecific interactions. Proc Natl Acad Sci U S A, 121(20):e2317373121 PubMed ID: 38722810
Summary: In many organisms, most notably Drosophila, homologous chromosomes associate in somatic cells, a phenomenon known as somatic pairing, which takes place without double strand breaks or strand invasion, thus requiring some other mechanism for homologs to recognize each other. Several studies have suggested a "specific button" model, in which a series of distinct regions in the genome, known as buttons, can associate with each other, mediated by different proteins that bind to these different regions. This study used computational modeling to evaluate an alternative "button barcode" model, in which there is only one type of recognition site or adhesion button, present in many copies in the genome, each of which can associate with any of the others with equal affinity. In this model, buttons are nonuniformly distributed, such that alignment of a chromosome with its correct homolog, compared with a nonhomolog, is energetically favored; since to achieve nonhomologous alignment, chromosomes would be required to mechanically deform in order to bring their buttons into mutual register. By simulating randomly generated nonuniform button distributions, many highly effective button barcodes can be easily found, some of which achieve virtually perfect pairing fidelity. This model is consistent with existing literature on the effect of translocations of different sizes on homolog pairing. It is conclude that a button barcode model can attain highly specific homolog recognition, comparable to that seen in actual cells undergoing somatic homolog pairing, without the need for specific interactions. This model may have implications for how meiotic pairing is achieved. | Hughes, S. E., Price, A., Briggs, S., Staber, C., James, M., Anderson, M., Hawley, R. S. (2024). A transcriptomics-based RNAi screen for regulators of meiosis and early stages of oocyte development in Drosophila melanogaster.G3 (Bethesda), 14(4) PubMed ID: 38333961
Summary: A properly regulated series of developmental and meiotic events must occur to ensure the successful production of gametes. In Drosophila melanogaster ovaries, these early developmental and meiotic events include the production of the 16-cell cyst, meiotic entry, synaptonemal complex (SC) formation, recombination, and oocyte specification. In order to identify additional genes involved in early oocyte development and meiosis, 3 published single-cell RNA-seq datasets from Drosophila ovaries were analyzed, using vasa (germline) together with c(3)G, cona, and corolla (SC) as markers. This analysis generated a 526 available RNAi lines containing shRNA constructs were in germline-compatible vectors representing 331 of the top 500 genes.Targeted ovaries were assessed for SC formation and maintenance, oocyte specification, cyst development, and double-strand break dynamics. Six uncharacterized genes exhibited early developmental defects. SC and developmental defects were observed for additional genes not well characterized in the early ovary. Interestingly, in some lines with developmental delays, meiotic events could still be completed once oocyte specificity occurred indicating plasticity in meiotic timing. These data indicate that a transcriptomics approach can be used to identify genes involved in functions in a specific cell type in the Drosophila ovary. |
| Vasavan, B., Das, N., Kahnamouei, P., Trombley, C., Swan, A. (2024). Skp2-Cyclin A Interaction Is Necessary for Mitotic Entry and Maintenance of Diploidy. J Mol Biol, 436(8):168505 PubMed ID: 38423454
Summary: Skp2, the substrate recognition component of the SCF(Skp2) ubiquitin ligase, has been implicated in the targeted destruction of a number of key cell cycle regulators and the promotion of S-phase. One of its critical targets is the Cyclin dependent kinase (Cdk) inhibitor p27 (Drosophila Dacapo), and indeed the overexpression of Skp2 in a number of cancers is directly correlated with the premature degradation of p27. Skp2 was first identified as a protein that interacts with Cyclin A in transformed cells, but its role in this complex has remained unclear. This paper demonstrates that Skp2 interacts with Cyclin A in Drosophila and is required to maintain Cyclin A levels and permit mitotic entry. Failure of mitotic entry in Skp2 mutant cells results in polyploidy. If these cells enter mitosis again they are unable to properly segregate their chromosomes, leading to checkpoint dependent cell cycle arrest or apoptosis. Thus, Skp2 is required for mitosis and for maintaining diploidy and genome stability. | Huang, Y. T., Hesting, L. L., Calvi, B. R. (2024). An unscheduled switch to endocycles induces a reversible senescent arrest that impairs growth of the Drosophila wing disc bioRxiv, PubMed ID: 38559130
Summary: A programmed developmental switch to G / S endocycles results in tissue growth through an increase in cell size. Unscheduled, induced endocycling cells (iECs) promote wound healing but also contribute to cancer. Much remains unknown, however, about how these iECs affect tissue growth. Using the D. melanogaster wing disc as model, this study found that populations of iECs initially increase in size but then subsequently undergo a heterogenous arrest that causes severe tissue undergrowth. iECs acquired DNA damage and activated a Jun N-terminal kinase (JNK) pathway, but, unlike other stressed cells, were apoptosis-resistant and not eliminated from the epithelium. Instead, iECs entered a JNK-dependent and reversible senescent-like arrest. Senescent iECs promoted division of diploid neighbors, but this compensatory proliferation did not rescue tissue growth. This study has uncovered unique attributes of iECs and their effects on tissue growth that have important implications for understanding their roles in wound healing and cancer. |
Thursday, March 6th - Disease Models |
| Polet, S. S., de Koning, T. J., Lambrechts, R. A., Tijssen, M. A. J., Sibon, O. C. M., Gorter, J. A. (2024). Conventional and novel anti-seizure medications reveal a particular role for GABA(A) in a North Sea progressive myoclonus Epilepsy Drosophila model. Epilepsy research, 203:107380 PubMed ID: 38781737
Summary: North Sea Progressive Myoclonus Epilepsy (NS-PME) is a rare genetic disorder characterized by ataxia, myoclonus and seizures with a progressive course. Although the cause of NS-PME is known, namely a homozygous mutation in the GOSR2 gene (c.430 G>T; p. Gly144Trp), sufficient treatment is lacking. Despite combinations of on average 3-5 anti-seizure medications (ASMs), debilitating myoclonus and seizures persist. This study aimed to gain insight into the most effective anti-convulsive target in NS-PME by evaluating the individual effects of ASMs in a NS-PME Drosophila model. A previously generated Drosophila model for NS-PME was used displaying progressive heat-sensitive seizures. This model was used to test 1. a first-generation ASM (sodium barbital), 2. common ASMs used in NS-PME (clonazepam, valproic acid, levetiracetam, ethosuximide) and 3. a novel third-generation ASM (ganaxolone) with similar mode of action to sodium barbital. Compounds were administered by adding them to the food in a range of concentrations. After 7 days of treatment, the percentage of heat-induced seizures was determined and compared to non-treated but affected controls. As previously reported in the NS-PME Drosophila model, sodium barbital resulted in significant seizure suppression, with increasing effect at higher dosages. Of the commonly prescribed ASMs, clonazepam and ethosuximide resulted in significant seizure suppression, whereas both valproic acid and levetiracetam did not show any changes in seizures. Interestingly, ganaxolone did result in seizure suppression as well. Of the six drugs tested, three of the four that resulted in seizure suppression (sodium barbital, clonazepam, ganaxolone) are primary known for their direct effect on GABA(A) receptors. This suggests that GABA(A) could be a potentially important target in the treatment of NS-PME. Consequently, these findings add rationale to the exploration of the clinical effect of ganaxolone in NS-PME and other progressive myoclonus epilepsies. | Dubey, P. K., Singh, S., Khalil, H., Kommini, G. K., Bhat, K. M., Krishnamurthy, P. (2024). Obg-like ATPase 1 Genetic Deletion Leads to Dilated Cardiomyopathy in Mice and Structural Changes in Drosophila Heart. bioRxiv, PubMed ID: 38854005
Summary: Cardiomyopathy, disease of the heart muscle, is a significant contributor to heart failure. The pathogenesis of cardiomyopathy is multifactorial and involves genetic, environmental, and lifestyle factors. Identifying and characterizing novel genes that contribute to cardiac pathophysiology are crucial for understanding cardiomyopathy and effective therapies. This study investigated the role of a novel gene, Obg-like ATPase 1 ( Ola1 ), in cardiac pathophysiology using a cardiac-specific knockout mouse model as well as a Drosophila model (see CG1354). Previous work demonstrated that OLA1 modulates the hypertrophic response of cardiomyocytes through the GSK-beta/beta-catenin signaling pathway. Furthermore, recent studies have suggested that OLA1 plays a critical role in organismal growth and development. For example, Ola1 null mice exhibit increased heart size and growth retardation. It is not known, however, if loss of function for Ola1 leads to dilated cardiomyopathy. Cardiac-specific Ola1 knockout mice (OLA1-cKO) were generated to evaluate the role of OLA1 in cardiac pathophysiology. Ola1-cKO in mice leads to dilated cardiomyopathy (DCM) and left ventricular (LV) dysfunction. These mice developed severe LV dilatation, thinning of the LV wall, reduced LV function, and, in some cases, ventricular wall rupture and death. In Drosophila, RNAi-mediated knock-down specifically in developing heart cells led to the change in the structure of pericardial cells from round to elongated, and abnormal heart function. This also caused significant growth reduction and pupal lethality. Thus, these findings suggest that OLA1 is critical for cardiac homeostasis and that its deficiency leads to dilated cardiomyopathy and dysfunction. Furthermore, this study highlights the potential of the Ola1 gene as a therapeutic target for dilated cardiomyopathy and heart failure. |
| Lewis, S. A., Forstrom, J., Tavani, J., Schafer, R., Tiede, Z., Padilla-Lopez, S. R., Kruer, M. C. (2024). eIF2alpha phosphorylation evokes dystonia-like movements with D2-receptor and cholinergic origin and abnormal neuronal connectivity. bioRxiv, PubMed ID: 38798458
Summary: Dystonia is the 3(rd) most common movement disorder. Dystonia is acquired through either injury or genetic mutations, with poorly understood molecular and cellular mechanisms. Eukaryotic initiation factor alpha (eIF2α) controls cell state including neuronal plasticity via protein translation control and expression of ATF4. Dysregulated eIF2α phosphorylation (eIF2α-P) occurs in dystonia patients and models including DYT1 (Drosophila Torsin), but the consequences are unknown. This study increased/decreased eIF2α-P and tested motor control and neuronal properties in a Drosophila model. Bidirectionally altering eIF2α-P produced dystonia-like abnormal posturing and dyskinetic movements in flies. These movements were also observed with expression of the DYT1 risk allele. Cholinergic and D2-receptor neuroanatomical origins were identified of these dyskinetic movements caused by genetic manipulations to dystonia molecular candidates eIF2α-P, ATF4, or DYT1, with evidence for decreased cholinergic release. In vivo, increased and decreased eIF2α-P increase synaptic connectivity at the NMJ with increased terminal size and bouton synaptic release sites. Long-term treatment of elevated eIF2α-P with ISRIB restored adult longevity, but not performance in a motor assay. Disrupted eIF2α-P signaling may alter neuronal connectivity, change synaptic release, and drive motor circuit changes in dystonia. | Yuan, Y., Yu, L., Zhuang, X., Wen, D., He, J., Hong, J., Xie, J., Ling, S., Du, X., Chen, W., Wang, X. (2025). Drosophila models used to simulate human ATP1A1 gene mutations that cause Charcot-Marie-Tooth type 2 disease and refractory seizures. Neural Regen Res, 20(1):265-276 PubMed ID: 38767491
Summary: Certain amino acids changes in the human Na+/K+-ATPase pump, ATPase Na+/K+ transporting subunit alpha 1 (ATP1A1), cause Charcot-Marie-Tooth disease type 2 (CMT2) disease and refractory seizures. To develop in vivo models to study the role of Na+/K+-ATPase in these diseases, the Drosophila gene homolog, Atpα, was modified to mimic the human ATP1A1 gene mutations that cause CMT2. Mutations located within the helical linker region of human ATP1A1 (I592T, A597T, P600T, and D601F) were simultaneously introduced into endogenous Drosophila Atpα by CRISPR/Cas9-mediated genome editing, generating the AtpαTTTF model. In addition, the same strategy was used to generate the corresponding single point mutations in flies (AtpαI571T, AtpαA576T, AtpαP579T, and AtpαD580F). Moreover, a deletion mutation (Atpαmut) that causes premature termination of translation was generated as a positive control. Of these alleles, two were found that could be maintained as homozygotes (AtpαI571T and AtpαP579T). Three alleles (AtpαA576T, AtpαP579 and AtpαD580F) can form heterozygotes with the Atpαmut allele. The Atpα allele carrying these CMT2-associated mutations showed differential phenotypes in Drosophila. Flies heterozygous for AtpαTTTF mutations have motor performance defects, a reduced lifespan, seizures, and an abnormal neuronal morphology. These Drosophila models will provide a new platform for studying the function and regulation of the sodium-potassium pump. |
| Sodders, M. J., Avila-Pacheco, J., Okorie, E. C., Shen, M., Kumari, N., Marathi, A., Lakhani, M., Bullock, K., Pierce, K., Dennis, C., Jeanfavre, S., Sarkar, S., Scherzer, C. R., Clish, C., Olsen, A. L. (2024). Genetic screening and metabolomics identify glial adenosine metabolism as a therapeutic target in Parkinson's disease. bioRxiv, PubMed ID: 38798570
Summary: Parkinson's disease (PD) is the second most common neurodegenerative disorder and lacks disease-modifying therapies. A Drosophila model has been developed for identifying novel glial-based therapeutic targets for PD. Human alpha-synuclein is expressed in neurons and individual genes are independently knocked down in glia. A forward genetic screen was conducted, knocking down the entire Drosophila kinome in glia in alpha-synuclein expressing flies. Among the top hits were five genes (9Ak1, (Ak6, Adk1, Adk2, and awd) involved in adenosine metabolism. Knockdown of each gene improved locomotor dysfunction, rescued neurodegeneration, and increased brain adenosine levels. It was determined that the mechanism of neuroprotection involves adenosine itself, as opposed to a downstream metabolite. Deeper undersrtanding was obtained into the mechanism for one gene, Ak1, finding rescue of dopaminergic neuron loss, alpha-synuclein aggregation, and bioenergetic dysfunction after glial Ak1 knockdown. Metabolomics was performed in Drosophila and in human PD patients, allowing comprehensive characterization of changes in purine metabolism and potential biomarkers of dysfunctional adenosine metabolism were identified in people. These experiments support glial adenosine as a novel therapeutic target in PD. | Chauvin, S. D., Ando, S., Holley, J. A., ..., Onodera, O., Kato, T., Miner, J. J. (2024). Inherited C-terminal TREX1 variants disrupt homology-directed repair to cause senescence and DNA damage phenotypes in Drosophila, mice, and humans. Nat Commun, 15(1):4696 PubMed ID: 38824133
Summary: Age-related microangiopathy, also known as small vessel disease (SVD), causes damage to the brain, retina, liver, and kidney. Based on the DNA damage theory of aging, it was reasoned that genomic instability may underlie an SVD caused by dominant C-terminal variants in TREX1, the most abundant 3'-5' DNA exonuclease in mammals. C-terminal TREX1 variants cause an adult-onset SVD known as retinal vasculopathy with cerebral leukoencephalopathy (RVCL or RVCL-S). In RVCL, an aberrant, C-terminally truncated TREX1 mislocalizes to the nucleus due to deletion of its ER-anchoring domain. Since RVCL pathology mimics that of radiation injury, it was reasoned that nuclear TREX1 would cause DNA damage. This study shows that RVCL-associated TREX1 variants trigger DNA damage in humans, mice, and Drosophila, and that cells expressing RVCL mutant TREX1 are more vulnerable to DNA damage induced by chemotherapy and cytokines that up-regulate TREX1, leading to depletion of TREX1-high cells in RVCL mice. RVCL-associated TREX1 mutants inhibit homology-directed repair (HDR), causing DNA deletions and vulnerablility to PARP inhibitors. In women with RVCL, early-onset breast cancer was observed, similar to patients with BRCA1/2 variants. These results provide a mechanistic basis linking aberrant TREX1 activity to the DNA damage theory of aging, premature senescence, and microvascular disease. |
Wednesday, March 5th - Adult physiology and metabolism |
| Wilkin, M. B., Whiteford, R., Akbar, T., Hosseini-Alghaderi, S., Revici, R., Carbery, A. M., Baron, M. (2024). The First Defined Null Allele of the Notch Regulator, a Suppressor of Deltex: Uncovering Its Novel Roles in Drosophila melanogaster Oogenesis. Biomolecules, 14(5) PubMed ID: 38785929
Summary: Suppressor of deltex (Su(dx)) is a Drosophila melanogaster member of the NEDD4 family of the HECT domain E3 ubiquitin ligases. Su(dx) acts as a regulator of Notch endocytic trafficking, promoting Notch lysosomal degradation and the down-regulation of both ligand-dependent and ligand-independent signalling, the latter involving trafficking through the endocytic pathway and activation of the endo/lysosomal membrane. Mutations of Su(dx) result in developmental phenotypes in the Drosophila wing that reflect increased Notch signalling, leading to gaps in the specification of the wing veins, and Su(dx) functions to provide the developmental robustness of Notch activity to environmental temperature shifts. The full developmental functions of Su(dx) are unclear; however, this is due to a lack of a clearly defined null allele. This study reports the first defined null mutation of Su(dx), generated by P-element excision, which removes the complete open reading frame. The mutation is recessive-viable, with the Notch gain of function phenotypes affecting wing vein and leg development. New roles were uncovered for Su(dx) in Drosophila oogenesis, where it regulates interfollicular stalk formation, egg chamber separation and germline cyst enwrapment by the follicle stem cells. Interestingly, while the null allele exhibited a gain in Notch activity during oogenesis, the previously described Su(dx)(SP) allele, which carries a seven amino acid in-frame deletion, displayed a Notch loss of function phenotypes and an increase in follicle stem cell turnover. This is despite both alleles displaying similar Notch gain of function in wing development. This unexpected context-dependent outcome of Su(dx)(sp) is thought to being due to the partial retention of function by the intact C2 and WW domain regions of the protein. These results extend understanding of the developmental role of Su(dx) in the tissue renewal and homeostasis of the Drosophila ovary and illustrate the importance of examining an allelic series of mutations to fully understand developmental functions. | Hemba-Waduge, R. U., Liu, M., Li, X., Sun, J. L., Budslick, E. A., Bondos, S. E., Ji, J. Y. (2024). Metabolic control by the Bithorax Complex-Wnt signaling crosstalk in Drosophila. bioRxiv, PubMed ID: 38853890
Summary: Adipocytes distributed throughout the body play crucial roles in lipid metabolism and energy homeostasis. Regional differences among adipocytes influence normal function and disease susceptibility, but the mechanisms driving this regional heterogeneity remain poorly understood. This study reports a genetic crosstalk between the Bithorax Complex ( BX-C ) genes and Wnt/Wingless signaling that orchestrates regional differences among adipocytes in Drosophila larvae. Abdominal adipocytes, characterized by the exclusive expression of abdominal A ( abd-A )and Abdominal B ( Abd-B ), exhibit distinct features compared to thoracic adipocytes, with Wnt signaling further amplifying these disparities. Depletion of BX-C genes in adipocytes reduces fat accumulation, delays larval-pupal transition, and eventually leads to pupal lethality. Depleting Abd-A or Abd-B reduces Wnt target gene expression, thereby attenuating Wnt signaling-induced lipid mobilization. Conversely, Wnt signaling stimulated abd-A transcription, suggesting a feedforward loop that amplifies the interplay between Wnt signaling and BX-C in adipocytes. These findings elucidate how the crosstalk between cell-autonomous BX-C gene expression and Wnt signaling define unique metabolic behaviors in adipocytes in different anatomical regions of fat body, delineating larval adipose tissue domains. |
| Zhang, T., Zhou, Q., Jusic, N., Lu, W., Pignoni, F., Neal, S. J. (2024). Mitf, with Yki and STRIPAK-PP2A, is a key determinant of form and fate in the progenitor epithelium of the Drosophila eye. European journal of cell biology, 103(2):151421 PubMed ID: 38776620
Summary: The Microphthalmia-associated Transcription Factor (MITF) governs numerous cellular and developmental processes. In mice, it promotes specification and differentiation of the retinal pigmented epithelium (RPE), and in humans, some mutations in MITF induce congenital eye malformations. This study explored the function and regulation of Mitf in Drosophila eye development, and two roles were uncovered. Knockdown of Mitf results in retinal displacement (RDis), a phenotype associated with abnormal eye formation. Mitf functions in the peripodial epithelium (PE), a retinal support tissue akin to the RPE, to suppress RDis, via the effector Yorkie (Yki). Yki physically interacts with Mitf and can modify its transcriptional activity in vitro. Severe loss of Mitf, instead, results in the de-repression of retinogenesis in the PE, precluding its development. This activity of Mitf requires the protein phosphatase 2 A holoenzyme STRIPAK-PP2A, but not Yki; Mitf transcriptional activity is potentiated by STRIPAK-PP2A in vitro and in vivo. Knockdown of STRIPAK-PP2A results in cytoplasmic retention of Mitf in vivo and in its decreased stability in vitro, highlighting two potential mechanisms for the control of Mitf function by STRIPAK-PP2A. Thus, Mitf functions in a context-dependent manner as a key determinant of form and fate in the Drosophila eye progenitor epithelium. | Zhai, C., Wang, Y., Qi, S., Yang, M., Wu, S. (2024). Yki stability and activity are regulated by Ca(2+)-calpains axis in Drosophila. J Genet Genomics, PubMed ID: 38663479
Summary: Yorkie (Yki) is a key effector of the Hippo pathway that activates the expression of targets by associating with the transcription factor Scalloped. Various upstream signals, such as cell polarity and mechanical cues, control transcriptional programs by regulating Yki activity. Searching for Yki regulatory factors has far-reaching significance for studying the Hippo pathway in animal development and human diseases. This study identified Calpain-A (CalpA) and Calpain-B (CalpB), two calcium (Ca(2+))-dependent modulatory proteases of the calpain family, as critical regulators of Yki in Drosophila that interact with Yki, respectively. Ca(2+) induces Yki cleavage in a CalpA/CalpB-dependent manner, and the protease activity of CalpA/CalpB is pivotal for the cleavage. Furthermore, overexpression of CalpA or CalpB in Drosophila partially restores the large wing phenotype caused by Yki overexpression, and F98 of Yki is an important cleavage site by the Ca(2+)-calpains axis. This study uncovers a unique mechanism whereby the Ca(2+)-calpain axis modulates Yki activity through protein cleavage. |
| Nuga, O., Richardson, K., Patel, N. C., Wang, X., Pagala, V., Stephan, A., Peng, J., Demontis, F., Todi, S. V. (2024). Linear poly-ubiquitin remodels the proteome and influences hundreds of regulators in Drosophila. G3 (Bethesda), 14(11) PubMed ID: 39325835
Summary: Ubiquitin controls many cellular processes via its post-translational conjugation onto substrates. Its use is highly variable due to its ability to form poly-ubiquitin with various topologies. Among them, linear chains have emerged as important regulators of immune responses and protein degradation. Previous studies in Drosophila melanogaster found that expression of linear poly-ubiquitin that cannot be dismantled into single moieties leads to their own ubiquitination and degradation or, alternatively, to their conjugation onto proteins. However, it remains largely unknown which proteins are sensitive to linear poly-ubiquitin. To address this question, this study expanded the toolkit to modulate linear chains and conducted ultra-deep coverage proteomics from flies that express non-cleavable, linear chains comprising 2, 4, or 6 moieties. These chains were found to regulate shared and distinct cellular processes in Drosophila by impacting hundreds of proteins. Theseresults provide key insight into the proteome subsets and cellular pathways that are influenced by linear poly-ubiquitin with distinct lengths and suggest that the ubiquitin system is exceedingly pliable. | Terry, D., Schweibenz, C., Moberg, K. (2024). Local Ecdysone synthesis in a wounded epithelium sustains developmental delay and promotes regeneration in Drosophila. Development, 151(12) PubMed ID: 38775023
Summary: Regenerative ability often declines as animals mature past embryonic and juvenile stages, suggesting that regeneration requires redirection of growth pathways that promote developmental growth. Intriguingly, the Drosophila larval epithelia require the hormone ecdysone (Ec) for growth but require a drop in circulating Ec levels to regenerate. Examining Ec dynamics more closely, this study found that transcriptional activity of the Ec-receptor (EcR) drops in uninjured regions of wing discs, but simultaneously rises in cells around the injury-induced blastema. In parallel, blastema depletion of genes encoding Ec biosynthesis enzymes blocks EcR activity and impairs regeneration but has no effect on uninjured wings. Local Ec/EcR signaling was found to be required for injury-induced pupariation delay following injury and that key regeneration regulators upd3 and Ets21c respond to Ec levels. Collectively, these data indicate that injury induces a local source of Ec within the wing blastema that sustains a transcriptional signature necessary for developmental delay and tissue repair. |
Tuesday, March 4th - Spermatogenesis |
| Tian, S., Nguyen, H., Ye, Z., Rouskin, S., Thirumalai, D., Trcek, T. (2024). The Folding of Germ Granule mRNAs Controls Intermolecular Base Pairing in Germ Granules and Maintains Normal Fly Development. bioRxiv, PubMed ID: 38853845
Summary: Drosophila germ granules enrich mRNAs critical for fly development. Within germ granules, mRNAs form multi-transcript clusters marked by increased mRNA concentration, creating an elevated potential for intermolecular base pairing. However, the type and abundance of intermolecular base pairing in mRNA clusters is poorly characterized. Using single-molecule super-resolution microscopy, chemical probing for base accessibility, phase separation assays, and simulations, mRNAs were demonstrated t remain well-folded upon localization to germ granules. While most base pairing is intramolecular, mRNAs still display the ability for intermolecular base pairing, facilitating clustering without high sequence complementarity or significant melting of secondary structure. This base pairing among mRNAs is driven by scattered and discontinuous stretches of bases appearing on the surface of folded RNAs, providing multivalency to clustering but exhibits low probability for sustained interactions. Notably, engineered germ granule mRNAs with exposed GC-rich complementary sequences (CSs) presented within stable stem loops induce sustained base pairing in vitro and enhanced intermolecular interactions in vivo. However, the presence of these stem loops alone disrupts fly development, and the addition of GC-rich CSs exacerbates this phenotype. Although germ granule mRNAs contain numerous GC-rich CSs capable of stable intermolecular base pairing, they are primarily embedded by RNA folding. This study emphasizes the role of RNA folding in controlling the type and abundance of intermolecular base pairing, thereby preserving the functional integrity of mRNAs within the germ granules. | Chao, C. F., Pesch, Y. Y., Yu, H., Wang, C., Aristizabal, M. J., Huan, T., Tanentzapf, G., Rideout, E. (2024). An important role for triglyceride in regulating spermatogenesis. Elife, 12 PubMed ID: 38805376
Summary: Drosophila is a powerful model to study how lipids affect spermatogenesis. Yet, the contribution of neutral lipids, a major lipid group which resides in organelles called lipid droplets (LD), to sperm development is largely unknown. Emerging evidence suggests LD are present in the testis and that loss of neutral lipid- and LD-associated genes causes subfertility; however, key regulators of testis neutral lipids and LD remain unclear. This stuey shows LD are present in early-stage somatic and germline cells within the Drosophila testis. A role was identified for triglyceride lipase brummer (bmm) in regulating testis LD; whole-body loss of bmm leads to defects in sperm development. Importantly, these represent cell-autonomous roles for bmm in regulating testis LD and spermatogenesis. Because lipidomic analysis of bmm mutants revealed excess triglyceride accumulation, and spermatogenic defects in bmm mutants were rescued by genetically blocking triglyceride synthesis, these data suggest that bmm-mediated regulation of triglyceride influences sperm development. This identifies triglyceride as an important neutral lipid that contributes to Drosophila sperm development, and reveals a key role for bmm in regulating testis triglyceride levels during spermatogenesis. |
| Roach, T. V., Lenhart, K. F. (2024). Mating-induced Ecdysone in the testis disrupts soma-germline contacts and stem cell cytokinesis. Development, 151(11) PubMed ID: 38832826
Summary: Germline maintenance relies on adult stem cells to continually replenish lost gametes over a lifetime and respond to external cues altering the demands on the tissue. Mating worsens germline homeostasis over time, yet a negative impact on stem cell behavior has not been explored. Using extended live imaging of the Drosophila testis stem cell niche, short periods of mating in young males was found to disrupt cytokinesis in germline stem cells (GSCs). This defect leads to failure of abscission, preventing release of differentiating cells from the niche. GSC abscission failure is caused by increased Ecdysone hormone signaling induced upon mating, which leads to disrupted somatic encystment of the germline. Abscission failure is rescued by isolating males from females, but recurs with resumption of mating. Importantly, reiterative mating also leads to increased GSC loss, requiring increased restoration of stem cells via symmetric renewal and de-differentiation. Together, these results suggest a model whereby acute mating results in hormonal changes that negatively impact GSC cytokinesis but preserves the stem cell population. | He, L., Sun, F., Wu, Y., Li, Z., Fu, Y., Huang, Q., Li, J., Wang, Z., Cai, J., Feng, C., Deng, X., Gu, H., He, X., Yu, J., Sun, F. (2024). L(1)10Bb serves as a conservative determinant for soma-germline communications via cellular non-autonomous effects within the testicular stem cell niche. Molecular and cellular endocrinology, 591:112278 PubMed ID: 38795826
Summary: The testicular stem cell niche is the central regulator of spermatogenesis in Drosophila melanogaster. However, the underlying regulatory mechanisms arwe unclear. This study demonstrated the crucial role of lethal (1) 10Bb [l(1)10Bb] in regulating the testicular stem cell niche. Dysfunction of l(1)10Bb in early-stage cyst cells led to male fertility disorders and compromised cyst stem cell maintenance. Moreover, the dysfunction of l(1)10Bb in early-stage cyst cells exerted non-autonomous effects on germline stem cell differentiation, independently of hub signals. Notably, this study highlights the rescue of testicular defects through ectopic expression of L(1)10Bb and the human homologous protein BUD31 homolog (BUD31). In addition, l(1)10Bb dysfunction in early-stage cyst cells downregulated the expression of spliceosome subunits in the Sm and the precursor RNA processing complexes. Collectively, these findings established l(1)10Bb as a pivotal factor in the modulation of Drosophila soma-germline communications within the testicular stem cell niche. |
| Su, Q., Xu, B., Chen, X., Rokita, S. E. (2024). Misregulation of bromotyrosine compromises fertility in male Drosophila. Proc Natl Acad Sci U S A, 121(21):e2322501121 PubMed ID: 38748578
Summary: Biological regulation often depends on reversible reactions such as phosphorylation, acylation, methylation, and glycosylation, but rarely halogenation. A notable exception is the iodination and deiodination of thyroid hormones. This study reports detection of bromotyrosine and its subsequent debromination during Drosophila spermatogenesis. Bromotyrosine is not evident when Drosophila express a native flavin-dependent dehalogenase that is homologous to the enzyme responsible for iodide salvage from iodotyrosine in mammals. Deletion or suppression of the dehalogenase-encoding condet (cdt) gene in Drosophila allows bromotyrosine to accumulate with no detectable chloro- or iodotyrosine. The presence of bromotyrosine in the cdt mutant males disrupts sperm individualization and results in decreased fertility. Transgenic expression of the cdt gene in late-staged germ cells rescues this defect and enhances tolerance of male flies to bromotyrosine. These results are consistent with reversible halogenation affecting Drosophila spermatogenesis in a process that had previously eluded metabolomic, proteomic, and genomic analyses. | Shao, Z., Hu, J., Jandura, A., Wilk, R., Jachimowicz, M., Ma, L., Hu, C., Sundquist, A., Das, I., Samuel-Larbi, P., Brill, J. A., Krause, H. M. (2024). Spatially revealed roles for lncRNAs in Drosophila spermatogenesis, Y chromosome function and evolution. Nat Commun, 15(1):3806 PubMed ID: 38714658
Summary: Unlike coding genes, the number of lncRNA genes in organism genomes is relatively proportional to organism complexity. From plants to humans, the tissues with highest numbers and levels of lncRNA gene expression are the male reproductive organs. To learn why, a genome-wide analysis was initiated of Drosophila lncRNA spatial expression patterns in these tissues. The numbers of genes and levels of expression observed greatly exceed those previously reported, due largely to a preponderance of non-polyadenylated transcripts. In stark contrast to coding genes, the highest numbers of lncRNAs expressed are in post-meiotic spermatids. Correlations between expression levels, localization and previously performed genetic analyses indicate high levels of function and requirement. More focused analyses indicate that lncRNAs play major roles in evolution by controlling transposable element activities, Y chromosome gene expression and sperm construction. A new type of lncRNA-based particle found in seminal fluid may also contribute to reproductive outcomes. |
Friday, February 28th - Immune Response |
| Chen, J., Lin, G., Ma, K., Li, Z., LiEgeois, S., Ferrandon, D. (2024). A specific innate immune response silences the virulence of Pseudomonas aeruginosa in a latent infection model in the Drosophila melanogaster host. PLoS pathogens, 20(6):e1012252 PubMed ID: 38833496
Summary: Microbial pathogenicity often depends on the route of infection. For instance, P. aeruginosa or S. marcescens cause acute systemic infections when low numbers of bacteria are injected into D. melanogaster flies whereas flies succumb much slower to the continuous ingestion of these pathogens, even though both manage to escape from the gut compartment and reach the hemocoel. This study developed a latent P. aeruginosa infection model by feeding flies on the bacteria for a short period. The bacteria stably colonize internal tissues yet hardly cause any damage since latently-infected flies live almost as long as noninfected control flies. The apparently dormant bacteria display particular characteristics in terms of bacterial colony morphology, composition of the outer cell wall, and motility. The virulence of these bacteria can however be reactivated upon wounding the host. Melanization but not the cellular or the systemic humoral response is the predominant host defense that establishes latency and may coerce the bacteria to a dormant state. In addition, the lasting activation of the melanization responses in latently-infected flies provides a degree of protection to the host against a secondary fungal infection. Latent infection by an ingested pathogen protects against a variety of homologous or heterologous systemic secondary infectious challenges, a situation previously described for the endosymbiotic Wolbachia bacteria, a guard against viral infections. | Maurya, D., Rai, G., Mandal, D., Mondal, B. C. (2024). Transient caspase-mediated activation of caspase-activated DNase causes DNA damage required for phagocytic macrophage differentiation. Cell Rep, 43(5):114251 PubMed ID: 38761374
Summary: Phagocytic macrophages are crucial for innate immunity and tissue homeostasis. Most tissue-resident macrophages develop from embryonic precursors that populate every organ before birth to lifelong self-renew. However, the mechanisms for versatile macrophage differentiation remain unknown. This study used in vivo genetic and cell biological analysis of the Drosophila larval hematopoietic organ, the lymph gland that produces macrophages. The developmentally regulated transient activation of caspase-activated DNase (CAD)-mediated DNA strand breaks in intermediate progenitors is essential for macrophage differentiation. Insulin receptor-mediated PI3K/Akt signaling regulates the apoptosis signal-regulating kinase 1 (Ask1)/c-Jun kinase (JNK) axis to control sublethal levels of caspase activation, causing DNA strand breaks during macrophage development. Furthermore, caspase activity is also required for embryonic-origin macrophage development and efficient phagocytosis. This study provides insights into developmental signaling and CAD-mediated DNA strand breaks associated with multifunctional and heterogeneous macrophage differentiation. |
| Prakash, A., Fenner, F., Shit, B., Salminen, T. S., Monteith, K. M., Khan, I., Vale, P. F. (2024). IMD-mediated innate immune priming increases Drosophila survival and reduces pathogen transmission. PLoS pathogens, 20(6):e1012308 PubMed ID: 38857285
Summary: Invertebrates lack the immune machinery underlying vertebrate-like acquired immunity. However, in many insects past infection by the same pathogen can 'prime' the immune response, resulting in improved survival upon reinfection. This study investigated the mechanistic basis and epidemiological consequences of innate immune priming in the fruit fly Drosophila melanogaster when infected with the gram-negative bacterial pathogen Providencia rettgeri. Priming in response to P. rettgeri infection is a long-lasting and sexually dimorphic response. The epidemiological consequences of immune priming was further explored; it has the potential to curtail pathogen transmission by reducing pathogen shedding and spread. The enhanced survival of individuals previously exposed to a non-lethal bacterial inoculum coincided with a transient decrease in bacterial loads, and strong evidence is provided that the effect of priming requires the IMD-responsive antimicrobial-peptide Diptericin-B in the fat body. Further, While Diptericin B is the main effector of bacterial clearance, it is not sufficient for immune priming, which requires regulation of IMD by peptidoglycan recognition proteins. This work underscores the plasticity and complexity of invertebrate responses to infection, providing novel experimental evidence for the effects of innate immune priming on population-level epidemiological outcomes. | Li, Y., Sun, Y., Li, R., Zhou, H., Li, S., Jin, P. (2024). Genetic Screening Revealed the Negative Regulation of miR-310~313 Cluster Members on Imd Pathway during Gram-Negative Bacterial Infection in Drosophila. Genes, 15(5) PubMed ID: 38790230
Summary: Innate immune response is the first line of host defense against pathogenic microorganisms, and its excessive or insufficient activation is detrimental to the organism. Many individual microRNAs (miRNAs) have emerged as crucial post-transcriptional regulators of immune homeostasis in Drosophila melanogaster. However, the synergistical regulation of miRNAs located within a cluster on the Imd-immune pathway remains obscured. In this study, a genetic screening with 52 transgenic UAS-miRNAs was performed to identify ten miRNAs or miRNA clusters, including the miR310~313 cluster, which may function on Imd-dependent immune responses. The miRNA RT-qPCR analysis showed that the expression of miR-310~313 cluster members exhibited an increase at 6-12 h post E. coli infection. Furthermore, the overexpression of the miR-310~313 cluster impaired the Drosophila survival. And the overexpression of miR-310/311/312 reduced Dpt expression, an indication of Imd pathway induced by Gram-negative bacteria. Conversely, the knockdown of miR-310/311/312 led to increases in Dpt expression. The Luciferase reporter expression assays and RT-qPCR analysis confirmed that miR-310~313 cluster members directly co-targeted and inhibited Imd transcription. These findings reveal that the members of the miR-310~313 cluster synergistically inhibit Imd-dependent immune responses by co-targeting the Imd gene in Drosophila. |
| Zhou, H., Huang, Y., Jia, C., Pang, Y., Liu, L., Xu, Y., Jin, P., Qian, J., Ma, F. (2024). NF-κB factors cooperate with Su(Hw)/E4F1 to balance Drosophila/human immune responses via modulating dynamic expression of miR-210. Nucleic Acids Res, 52(12):6906-6927 PubMed ID: 38742642
Summary: MicroRNAs (miRNAs) play crucial regulatory roles in controlling immune responses, but their dynamic expression mechanisms are poorly understood. This study firstly confirm that the conserved miRNA miR-210 negatively regulates innate immune responses of Drosophila and human via targeting Toll and TLR6, respectively. Secondly, the findings of this study demonstrate that the expression of miR-210 is dynamically regulated by NF-κB factor Dorsal in immune response of Drosophila Toll pathway. Thirdly, we find that Dorsal-mediated transcriptional inhibition of miR-210 is dependent on the transcriptional repressor Su(Hw). Mechanistically, Dorsal interacts with Su(Hw) to modulate cooperatively the dynamic expression of miR-210 in a time- and dose-dependent manner, thereby controlling the strength of Drosophila Toll immune response and maintaining immune homeostasis. Fourthly, a similar mechanism was revealed in human cells, where NF-κB/RelA cooperates with E4F1 to regulate the dynamic expression of hsa-miR-210 in the TLR immune response. Overall, this study reveals a conservative regulatory mechanism that maintains animal innate immune homeostasis and provides new insights into the dynamic regulation of miRNA expression in immune response. | Zhou, H., Liu, L., Pang, Y., Xu, Y., Wu, J., Ma, F., Jin, P., Zhou, X. (2024). Relish-mediated C2H2 zinc finger protein IMZF restores Drosophila immune homeostasis via inhibiting the transcription of Imd/Tak1. Insect biochemistry and molecular biology, 170:104138 PubMed ID: 38762126
Summary: The dysregulation of intensity and duration in innate immunity can result in detrimental effects on the body, emphasizing the crucial need for precise regulation. However, the intricate and accurate nature of innate immunity implies the existence of numerous undiscovered innate immunomodulators, particularly transcription factors. In this study, we have identified a Drosophila C2H2 zinc finger protein CG18262, named Immune-mediated Zinc Finger protein (IMZF), capable of suppressing immune responses of Imd pathway. Mechanistically, IMZF serves as a transcription factor that represses the expression of Imd and Tak1. Intriguingly, our findings also reveal that Relish, an NF-κB transcription factor, positively regulates the expression of IMZF, consequently inhibiting the activation of Imd and Tak1 to prevent an exaggerated immune response. Additionally, we have elucidated the pivotal role played by the Relish-IMZF-Imd/Tak1 axis in restoring immune homeostasis of Drosophila Imd pathway. In summary, our findings not only unveil a novel C2H2 zinc finger immunoregulatory transcription factor, IMZF, along with its specific mechanism of immune regulation, but also shed light on the dual functionality of Relish in different stages of the immune response by modulating distinct effectors. This discovery provides new insights and enlightenment into the complex regulation of Drosophila innate immunity. |
Thursday, February 27th - Behavior |
| Gattuso, H., Nuñez, K., de la Rea, B., Ermentrout, B., Victor, J., Nagel, K. (2024). Inhibitory control of locomotor statistics in walking Drosophila. bioRxiv, PubMed ID: 38659800
Summary: In order to forage for food, many animals regulate not only specific limb movements but the statistics of locomotor behavior over time, for example switching between long-range dispersal behaviors and more localized search depending on the availability of resources. How pre-motor circuits regulate such locomotor statistics is not clear. This study took advantage of the robust changes in locomotor statistics evoked by attractive odors in walking Drosophila to investigate their neural control. The study began by analyzing the statistics of ground speed and angular velocity during three well-defined motor regimes: baseline walking, upwind running during odor, and search behavior following odor offset. During search behavior, flies adopt higher angular velocities and slower ground speeds, and tend to turn for longer periods of time in one direction. Flies spontaneously adopt periods of different mean ground speed, and these changes in state influence the length of odor-evoked runs. A simple physiologically-inspired computational model of locomotor control was developed that can recapitulate these statistical features of fly locomotion. The model suggests that contralateral inhibition plays a key role both in regulating the difference between baseline and search behavior, and in modulating the response to odor with ground speed. As the fly connectome predicts decussating inhibitory neurons in the lateral accessory lobe (LAL), a pre-motor structure, genetic tools were developed to target these neurons and test their role in behavior. Consistent with this model, Activation of neurons labeled in one line was found to increase curvature. In a second line labeling distinct neurons, activation and inactivation strongly and reciprocally regulated ground speed and altered the length of the odor-evoked run. Additional targeted light activation experiments argue that these effects arise from the brain rather than from neurons in the ventral nerve cord, while sparse activation experiments argue that speed control in the second line arises from both LAL neurons and a population of neurons in the dorsal superior medial protocerebrum (SMP). Together, this work develops a biologically plausible computational architecture that captures the statistical features of fly locomotion across behavioral states and identifies potential neural substrates of these computations. | Smithson, C. H., Duncan, E. J., Sait, S. M., Bretman, A. (2024). Sensory perception of rivals has trait-dependent effects on plasticity in Drosophila melanogaster. Behavioral ecology : official journal of the International Society for Behavioral Ecology, 35(3):arae031 PubMed ID: 38680228
Summary: The social environment has myriad effects on individuals, altering reproduction, immune function, cognition, and aging. Phenotypic plasticity enables animals to respond to heterogeneous environments such as the social environment but requires that they assess those environments accurately. It has been suggested that combinations of sensory cues allow animals to respond rapidly and accurately to changeable environments, but it is unclear whether the same sensory inputs are required in all traits that respond to a particular environmental cue. Drosophila melanogaster males, in the presence of rival males, exhibit a consistent behavioral response by extending mating duration. However, exposure to a rival also results in a reduction in their lifespan, a phenomenon interpreted as a trade-off associated with sperm competition strategies. D. melanogaster perceive their rivals by using multiple sensory cues; interfering with at least two olfactory, auditory, or tactihe cues eliminates the extension of mating duration. This study assessed whether these same cues were implicated in the lifespan reduction. Removal of combinations of auditory and olfactory cues removed the extended mating duration response to a rival, as previously found. However, these manipulations did not alter the reduction in lifespan of males exposed to rivals or induce any changes in activity patterns, grooming, or male-male aggression. Therefore, this analysis suggests that lifespan reduction is not a cost associated with the behavioral responses to sperm competition. Moreover, this highlights the trait-specific nature of the mechanisms underlying plasticity in response to the same environmental conditions. |
| Brand, J. A., Aich, U., Yee, W. K. W., Wong, B. B. M., Dowling, D. K. (2024). Sexual Selection Increases Male Behavioral Consistency in Drosophila melanogaster. The American naturalist, 203(6):713-725 PubMed ID: 38781526
Summary: Sexual selection has been suggested to influence the expression of male behavioral consistency. However, despite predictions, direct experimental support for this hypothesis has been lacking. Here, we investigated whether sexual selection altered male behavioral consistency in Drosophila melanogaster-a species with both pre- and postcopulatory sexual selection. We took 1,144 measures of locomotor activity (a fitness-related trait in D. melanogaster) from 286 flies derived from replicated populations that have experimentally evolved under either high or low levels of sexual selection for >320 generations. We found that high sexual selection males were more consistent (decreased within-individual variance) in their locomotor activity than male conspecifics from low sexual selection populations. There were no differences in behavioral consistency between females from the high and low sexual selection populations. Furthermore, while females were more behaviorally consistent than males in the low sexual selection populations, there were no sex differences in behavioral consistency in high sexual selection populations. Our results demonstrate that behavioral plasticity is reduced in males from populations exposed to high levels of sexual selection. Disentangling whether these effects represent an evolved response to changes in the intensity of selection or are manifested through nongenetic parental effects represents a challenge for future research. | Deluca, A., Bascom, B., Key Planas, D. A., Kocher, M. A., Torres, M., Arbeitman, M. N. (2024). Contribution of neurons that express fruitless and Clock transcription factors to behavioral rhythms and courtship. bioRxiv, PubMed ID: 38915619
Summary: Animals need to integrate information across neuronal networks that direct reproductive behaviors and circadian rhythms. In Drosophila, the master regulatory transcription factors that direct courtship behaviors and circadian rhythms are co-expressed in a small set of neurons. This study investigated the role of these neurons in both males and females. Sex-differences were found in the number of these fruitless and Clock -expressing neurons (fru ∩ Clk neurons) that is regulated by male-specific Fru. fru ∩ Clk neurons were assigned to the electron microscopy connectome that provides high resolution structural information. Sex-differences were asigned in the number of fru -expressing neurons that are post-synaptic targets of Clk -expressing neurons, with more post-synaptic targets in males. When fru cap; Clk neurons are activated or silenced, males have a shorter period length. Activation of fru cap; Clk neurons also changes the rate a courtship behavior is performed. Activation and silencing fru cap; Clk neurons impacts the molecular clock in the sLNv master pacemaker neurons, in a cell-nonautonomous manner. These results reveal how neurons that subserve the two processes, reproduction and circadian rhythms, can impact behavioral outcomes in a sex-specific manner. |
| Bidell, D., Feige, N. D., Triphan, T., Muller, C., Pauls, D., Helfrich-Forster, C., Selcho, M. (2024). Photoreceptors for immediate effects of light on circadian behavior. iScience, 27(6):109819 PubMed ID: 38770135
Summary: Animals need to sharpen their behavioral output in order to adapt to a variable environment. Hereby, light is one of the most pivotal environmental signals and thus behavioral plasticity in response to light can be observed in diurnal animals, including humans. Furthermore, light is the main entraining signal of the clock, yet immediate effects of light enhance or overwrite circadian output and thereby mask circadian behavior. In Drosophila, such masking effects are most evident as a lights-on response in two behavioral rhythms - the emergence of the adult insect from the pupa, called eclosion, and the diurnal rhythm of locomotor activity. This study shows that the immediate effect of light on eclosion depends solely on R8 photoreceptors of the eyes. In contrast, the increase in activity by light at night is triggered by different cells and organs that seem to compensate for the loss of each other, potentially to ensure behavioral plasticity. | Dan, C., Hulse, B. K., Kappagantula, R., Jayaraman, V., Hermundstad, A. M. (2024). A neural circuit architecture for rapid learning in goal-directed navigation. Neuron, 112(15):2581-2599. PubMed ID: 38795708
Summary: Anchoring goals to spatial representations enables flexible navigation but is challenging in novel environments when both representations must be acquired simultaneously. This paper proposes a framework for how Drosophila uses internal representations of head direction (HD) to build goal representations upon selective thermal reinforcement. Flies were shown use stochastically generated fixations and directed saccades to express heading preferences in an operant visual learning paradigm and that HD neurons are required to modify these preferences based on reinforcement. Ssymmetric visual setting was used to expose how flies' HD and goal representations co-evolve and how the reliability of these interacting representations impacts behavior. Finally, how rapid learning of new goal headings may rest on a behavioral policy whose parameters are flexible but whose form is genetically encoded in circuit architecture. Such evolutionarily structured architectures, which enable rapidly adaptive behavior driven by internal representations, may be relevant across species. |
Tuesday, February 25th - Adult Physiology and Metabolism |
| Blanchard, A., Aminot, M., Gould, N., Leger, A., Pichaud, N. (2024)Authors and Date. Flies on the rise: acclimation effect on mitochondrial oxidation capacity at normal and high temperatures in Drosophila melanogaster. The Journal of experimental biology, 227(12) PubMed ID: 38841909
Summary: Increased average temperatures and extreme thermal events (such as heatwaves) brought forth by climate change impose important constraints on aerobic metabolism. Notably, mitochondrial metabolism, which is affected by both long- and short-term temperature changes, has been put forward as an important determinant for thermal tolerance of organisms. This study examined the influence of phenotypic plasticity on metabolic and physiological parameters in Drosophila melanogaster and the link between mitochondrial function and their upper thermal limits. D. melanogaster acclimated to 15°C have a 0.65°C lower critical thermal maximum (CTmax) compared with those acclimated to 24°C. Drosophila melanogaster acclimated to 15°C exhibited a higher proportion of shorter saturated and monounsaturated fatty acids, concomitant with lower proportions of polyunsaturated fatty acids. No mitochondrial quantitative changes (fractional area and number) were detected between acclimation groups, but changes of mitochondrial oxidation capacities were observed. Specifically, in both 15°C- and 24°C-acclimated flies, complex I-induced respiration was increased when measured between 15 and 24°C, but drastically declined when measured at 4°°C. When succinate and glycerol-3-phosphate were added, this decrease was however compensated for in flies acclimated to 24°C, suggesting an important impact of acclimation on mitochondrial function related to thermal tolerance. This study reveals that the use of oxidative substrates at high temperatures is influenced by acclimation temperature and strongly related to upper thermal tolerance as a difference of 0.65°C in CTmax translates into significant mitochondrial changes. | Cai, Y. D., Chow, G. K., Hidalgo, S., Liu, X., Jackson, K. C., Vasquez, C. D., Gao, Z. Y., Lam, V. H., Tabuloc, C. A., Zheng, H., Zhao, C., Chiu, J. C. (2024). Alternative splicing of clock transcript mediates the response of circadian clocks to temperature changes. bioRxiv, PubMed ID: 38766142
Summary: Circadian clocks respond to temperature changes over the calendar year, allowing organisms to adjust their daily biological rhythms to optimize health and fitness. In Drosophila, seasonal adaptations and temperature compensation are regulated by temperature-sensitive alternative splicing (AS) of period (per) and timeless (tim) genes that encode key transcriptional repressors of clock gene expression. Although clock (clk) gene encodes the critical activator of clock gene expression, AS of its transcripts and its potential role in temperature regulation of clock function have not been explored. This study therefore sought to investigate whether clk exhibits AS in response to temperature and the functional changes of the differentially spliced transcripts. clk transcripts indeed undergo temperature-sensitive AS. Specifically, cold temperature leads to the production of an alternative clk transcript, hereinafter termed clk-cold, which encodes a CLK isoform with an in-frame deletion of four amino acids proximal to the DNA binding domain. Notably, serine 13 (S13), which was found to be a CCk1-dependent phosphorylation site, is among the four amino acids deleted in CLK-cold protein. Using a combination of transgenic fly, tissue culture, and in vitro experiments, it was demonstrated that upon phosphorylation at CLK(S13), CLK-DNA interaction is reduced, thus decreasing CLK occupancy at clock gene promoters. This is in agreement with findings that CLK occupancy at clock genes and transcriptional output are elevated at cold temperature, which can be explained by the higher amounts of CLK-cold isoforms that lack S13 residue. This study provides new insights into the complex collaboration between AS and phospho-regulation in shaping temperature responses of the circadian clock. |
| De Groef, S., Ribeiro Lopes, M., Winant, M., Rosschaert, E., Wilms, T., Bolckmans, L., Calevro, F., Callaerts, P. (2024). Reference genes to study the sex-biased expression of genes regulating Drosophila metabolism. Sci Rep, 14(1):9518 PubMed ID: 38664539
Summary: Sex is an important variable in biology. Notable differences have been observed between male and female Drosophila in regulation of metabolism, in response to nutritional challenges, and in phenotypes relevant for obesity and metabolic disorders. The differences between males and females can be expected to result from differences in gene expression. Expression levels of reference genes commonly used for normalization of qRT-PCR results such as GAPDH, β-actin, and 18SrRNA, show prominent sexual dimorphism. Since this will impact relative expression and conclusions related to that, a systematic analysis was performed of candidate reference genes with the objective of identifying reference genes with stable expression in male and female Drosophila. These reference genes (LamCa, βTub60D and βTub97EF) were then used to assess sex-specific differences in expression of metabolism associated genes. Additionally, the utility of these reference genes was evaluated following a nutritional challenge; LamCa and βtub97EF were shown to be stably expressed between sexes and under different nutritional conditions and are thus suitable as reference genes. The results highlight the importance of evaluating the stability of reference genes when sex-specific differences in gene expression are studied and identify structural genes as a category worth exploring as reference genes in other species. Finally, this study also uncovered hitherto unknown sexually dimorphic expression of a number of metabolism-associated genes, information of interest to others working in the field of metabolic disorders. | Malik, D. M., Rhoades, S. D., Kain, P., Sengupta, A., Sehgal, A., Weljie, A. M. (2024). Altered Metabolism during the Dark Period in Drosophila Short Sleep Mutants. Journal of proteome research, 23(9):3823-3836 PubMed ID: 38836855
Summary: Sleep is regulated via circadian mechanisms, but effects of sleep disruption on physiological rhythms, in particular metabolic cycling, remain unclear. To examine this question, diurnal metabolic alterations were probed of two Drosophila short sleep mutants, fumin and sleepless. Samples were collected with high temporal sampling (every 2 h) over 24 h under a 12:12 light:dark cycle, and profiling was done using an ion-switching LCMS/MS method. Fewer metabolites with 24 h oscillations were noted with short sleep (50 and 46 in fumin and sleepless, BH. Q < 0.2 by RAIN analysis) compared to a wild-type control (iso(31), 63 with BH. Q < 0.2), and peak phases of the sleep mutants were consolidated into two major phase peaks at mid-day and middle of night. Overall, altered nicotinate/nicotinamide, alanine/aspartate/glutamate, acetylcholine, glyoxylate/dicarboxylate, and TCA cycle metabolism were observed in the short sleep mutants, indicative of increased energetic demand and oxidative stress compared to wild type. Both changes in cycling and discriminant models suggest unique alterations in the dark period indicative of constrained metabolic networks. Thus, it is concluded that sleep loss alters metabolic function uniquely throughout the day, and further examination of specific mechanisms is warranted. |
| Xu, B., Hwangbo, D. S., Saurabh, S., Rosensweig, C., Allada, R., Kath, W. L., Braun, R. (2024). Temperature-driven coordination of circadian transcriptional regulation. PLoS Comput Biol, 20(4):e1012029 PubMed ID: 38648221
Summary: The circadian clock is an evolutionarily-conserved molecular oscillator that enables species to anticipate rhythmic changes in their environment. At a molecular level, the core clock genes induce circadian oscillations in thousands of genes in a tissue-specific manner, orchestrating myriad biological processes. While previous studies have investigated how the core clock circuit responds to environmental perturbations such as temperature, the downstream effects of such perturbations on circadian regulation remain poorly understood. By analyzing bulk-RNA sequencing of Drosophila fat bodies harvested from flies subjected to different environmental conditions, a highly condition-specific circadian transcriptome was demonstrated: genes are cycling in a temperature-specific manner, and the distributions of their phases also differ between the two conditions. Further employing a reference-based gene regulatory network (Reactome), evidence was found of increased gene-gene coordination at low temperatures and synchronization of rhythmic genes that are network neighbors. The phase differences between cycling genes increase as a function of geodesic distance in the low temperature condition was demonstrated, suggesting increased coordination of cycling on the gene regulatory network. These results suggest a potential mechanism whereby the circadian clock mediates the fly's response to seasonal changes in temperature. | Li, X., Yang, Y., Bai, X., Wang, X., Tan, H., Chen, Y., Zhu, Y., Liu, Q., Wu, M. N., Li, Y. (2024). A brain-derived insulin signal encodes protein satiety for nutrient-specific feeding inhibition. Cell Rep, 43(6):114282. PubMed ID: 38795342
Summary: The suppressive effect of insulin on food intake has been documented for decades. However, whether insulin signals can encode a certain type of nutrients to regulate nutrient-specific feeding behavior remains elusive. This study shows that in female Drosophila, a pair of dopaminergic neurons, tritocerebrum 1-dopaminergic neurons (T1-DANs), are directly activated by a protein-intake-induced insulin signal from insulin-producing cells (IPCs). Intriguingly, opto-activating IPCs elicits feeding inhibition for both protein and sugar, while silencing T1-DANs blocks this inhibition only for protein food. Elevating insulin signaling in T1-DANs or opto-activating these neurons is sufficient to mimic protein satiety. Furthermore, this signal is conveyed to local neurons of the protocerebral bridge (PB-LNs) and specifically suppresses protein intake. Therefore, these findings reveal that a brain-derived insulin signal encodes protein satiety and suppresses feeding behavior in a nutrient-specific manner, shedding light on the functional specificity of brain insulin signals in regulating behaviors. |
Friday, February 21st - Larval and Adult Neural Structure, Development, Function and Evolution |
| Contreras, E. G., Kautzmann, S., Klmmbt, C. (2024). The Drosophila blood-brain barrier invades the nervous system in a GPCR-dependent manner. Frontiers in cellular neuroscience, 18:1397627 PubMed ID: 38846639
Summary: The blood-brain barrier (BBB) represents a crucial interface between the circulatory system and the brain. In Drosophila melanogaster, the BBB is composed of perineurial and subperineurial glial cells. The perineurial glial cells are small mitotically active cells forming the outermost layer of the nervous system and are engaged in nutrient uptake. The subperineurial glial cells form occluding septate junctions to prevent paracellular diffusion of macromolecules into the nervous system. To address whether the subperineurial glia just form a simple barrier or whether they establish specific contacts with both the perineurial glial cells and inner central nervous system (CNS) cells, a detailed morphological analysis was undertaken. Using genetically encoded markers alongside with high-resolution laser scanning confocal microscopy and transmission electron microscopy, thin cell processes extending into the perineurial layer and into the CNS cortex were identified. Interestingly, long cell processes were observed reaching the glia ensheathing the neuropil of the central brain. GFP reconstitution experiments highlighted multiple regions of membrane contacts between subperineurial and ensheathing glia. Furthermore, we identify the G-protein-coupled receptor (GPCR) Moody as negative regulator of the growth of subperineurial cell processes. Loss of moody triggered a massive overgrowth of subperineurial cell processes into the CNS cortex and, moreover, affected the polarized localization of the xenobiotic transporter Mdr65. Finally, GPCR signaling, but not septate junction formation, was found to be is responsible for controlling membrane overgrowth. These findings support the notion that the Drosophila BBB is able to bridge the communication gap between circulation and synaptic regions of the brain by long cell processes. | Chitre, K., Kairamkonda, S., Dwivedi, M. K., Yadav, S., Kumar, V., Sikdar, S. K., Nongthomba, U. (2024). Beadex, the Drosophila LIM only protein, is required for the growth of the larval neuromuscular junction. Journal of neurophysiology, 132(2):418-432 PubMed ID: 38838299
Summary: The appropriate growth of the neurons, accurate organization of their synapses, and successful neurotransmission are indispensable for sensorimotor activities. These processes are highly dynamic and tightly regulated. Extensive genetic, molecular, physiological, and behavioral studies have identified many molecular candidates and investigated their roles in various neuromuscular processes. This study shows that Beadex (Bx), the Drosophila LIM only (LMO) protein, is required for motor activities and neuromuscular growth of Drosophila. The larvae bearing Bx7, a null allele of Bx, and the RNAi-mediated neuronal-specific knockdown of Bx show drastically reduced crawling behavior, a diminished synaptic span of the neuromuscular junctions (NMJs) and an increased spontaneous neuronal firing with altered motor patterns in the central pattern generators (CPGs). Microarray studies identified multiple targets of Beadex that are involved in different cellular and molecular pathways, including those associated with the cytoskeleton and mitochondria that could be responsible for the observed neuromuscular defects. With genetic interaction studies, it was further shown that Highwire (Hiw), a negative regulator of synaptic growth at the NMJs, negatively regulates Bx, as the latter's deficiency was able to rescue the phenotype of the Hiw null mutant, HiwDN. Thus, these data indicate that Beadex functions downstream of Hiw to regulate the larval synaptic growth and physiology. |
| Ellis, K. E., Bervoets, S., Smihula, H., Ganguly, I., Vigato, E., Auer, T. O., Benton, R., Litwin-Kumar, A., Caron, S. J. C. (2024). Evolution of connectivity architecture in the Drosophila mushroom body. Nat Commun, 15(1):4872 PubMed ID: 38849331
Summary: Brain evolution has primarily been studied at the macroscopic level by comparing the relative size of homologous brain centers between species. How neuronal circuits change at the cellular level over evolutionary time remains largely unanswered. Using a phylogenetically informed framework, this study compared the olfactory circuits of three closely related Drosophila species that differ in their chemical ecology: the generalists Drosophila melanogaster and Drosophila simulans and Drosophila sechellia that specializes on ripe noni fruit. A central part of the olfactory circuit that has not been investigated in these species-the connections between projection neurons and the Kenyon cells of the mushroom body- was examined and species-specific connectivity patterns were identified. Neurons encoding food odors connect more frequently with Kenyon cells, giving rise to species-specific biases in connectivity. These species-specific connectivity differences reflect two distinct neuronal phenotypes: in the number of projection neurons or in the number of presynaptic boutons formed by individual projection neurons. Finally, behavioral analyses suggest that such increased connectivity enhances learning performance in an associative task. This study shows how fine-grained aspects of connectivity architecture in an associative brain center can change during evolution to reflect the chemical ecology of a species. | Choi, K., Rosenbluth, W., Graf, I. R., Kadakia, N., Emonet, T. (2024). Bifurcation enhances temporal information encoding in the olfactory periphery. bioRxiv, PubMed ID: 38853849
Summary: Living systems continually respond to signals from the surrounding environment. Survival requires that their responses adapt quickly and robustly to the changes in the environment. One particularly challenging example is olfactory navigation in turbulent plumes, where animals experience highly intermittent odor signals while odor concentration varies over many length- and timescales. This study shows theoretically that Drosophila olfactory receptor neurons (ORNs) can exploit proximity to a bifurcation point of their firing dynamics to reliably extract information about the timing and intensity of fluctuations in the odor signal, which have been shown to be critical for odor-guided navigation. Close to the bifurcation, the system is intrinsically invariant to signal variance, and information about the timing, duration, and intensity of odor fluctuations is transferred efficiently. Importantly, we find that proximity to the bifurcation is maintained by mean adaptation alone and therefore does not require any additional feedback mechanism or fine-tuning. Using a biophysical model with calcium-based feedback, we demonstrate that this mechanism can explain the measured adaptation characteristics of Drosophila ORNs. |
| Lymer, S., Patel, K., Lennon, J., Blau, J. (2024). Circadian clock neurons use activity-regulated gene expression for structural plasticity. bioRxiv, PubMed ID: 38826237
Summary: Drosophila s-LNv circadian pacemaker neurons show dramatic structural plasticity, with their projections expanded at dawn and then retracted by dusk. This predictable plasticity makes s-LNvs ideal to study molecular mechanisms of plasticity. Although s-LNv plasticity is controlled by their molecular clock, changing s-LNv excitability also regulates plasticity. This study tested the idea that s-LNvs use activity-regulated genes to control plasticity. Inducing expression of either of the activity-regulated transcription factors Hr38 or Stripe (orthologs of mammalian Nr4a1 and Egr1) is sufficient to rapidly expand s-LNv projections. Conversely, transiently knocking down expression of either Hr38 or sr blocks expansion of s-LNv projections at dawn. t Hr38 rapidly induces transcription of sif, which encodes a Rac1 GEF required for s-LNv plasticity rhythms. It is concluded that the s-LNv molecular clock controls s-LNv excitability, which couples to an activity-regulated gene expression program to control s-LNv plasticity. | Meschi, E., Duquenoy, L., Otto, N., Dempsey, G., Waddell, S. (2024). Compensatory enhancement of input maintains aversive dopaminergic reinforcement in hungry Drosophila.. Neuron, 112(14):2315-2332.e2318 PubMed ID: 38795709
Summary: Hungry animals need compensatory mechanisms to maintain flexible brain function, while modulation reconfigures circuits to prioritize resource seeking. In Drosophila, hunger inhibits aversively reinforcing dopaminergic neurons (DANs) to permit the expression of food-seeking memories. Multitasking the reinforcement system for motivation potentially undermines aversive learning. We find that chronic hunger mildly enhances aversive learning and that satiated-baseline and hunger-enhanced learning require endocrine adipokinetic hormone (AKH) signaling. Circulating AKH influences aversive learning via its receptor in four neurons in the ventral brain, two of which are octopaminergic. Connectomics revealed AKH receptor-expressing neurons to be upstream of several classes of ascending neurons, many of which are presynaptic to aversively reinforcing DANs. Octopaminergic modulation of and output from at least one of these ascending pathways is required for shock- and bitter-taste-reinforced aversive learning. It is proposed that coordinated enhancement of input compensates for hunger-directed inhibition of aversive DANs to preserve reinforcement when required. |
Thursday, February 20th - Disease Models |
| Tsap, M. I., Yatsenko, A. S., Hegermann, J., Beckmann, B., Tsikas, D., Shcherbata, H. R. (2024). Unraveling the link between neuropathy target esterase NTE/SWS, lysosomal storage diseases, inflammation, abnormal fatty acid metabolism, and leaky brain barrier. Elife, 13 PubMed ID: 38660940
Summary: Mutations in Drosophila Swiss cheese (SWS) gene or its vertebrate orthologue neuropathy target esterase (NTE) lead to progressive neuronal degeneration in flies and humans. Despite its enzymatic function as a phospholipase is well established, the molecular mechanism responsible for maintaining nervous system integrity remains unclear. This study found that NTE/SWS is present in surface glia that forms the blood-brain barrier (BBB) and that NTE/SWS is important to maintain its structure and permeability. Importantly, BBB glia-specific expression of Drosophila NTE/SWS or human NTE in the sws mutant background fully rescues surface glial organization and partially restores BBB integrity, suggesting a conserved function of NTE/SWS. Interestingly, sws mutant glia showed abnormal organization of plasma membrane domains and tight junction rafts accompanied by the accumulation of lipid droplets, lysosomes, and multilamellar bodies. Since the observed cellular phenotypes closely resemble the characteristics described in a group of metabolic disorders known as lysosomal storage diseases (LSDs), these data established a novel connection between NTE/SWS and these conditions. Mutants with defective BBB exhibit elevated levels of fatty acids, which are precursors of eicosanoids and are involved in the inflammatory response. Also, as a consequence of a permeable BBB, several innate immunity factors are upregulated in an age-dependent Xmanner, while BBB glia-specific expression of NTE/SWS normalizes inflammatory response. Treatment with anti-inflammatory agents prevents the abnormal architecture of the BBB, suggesting that inflammation contributes to the maintenance of a healthy brain barrier. Considering the link between a malfunctioning BBB and various neurodegenerative diseases, gaining a deeper understanding of the molecular mechanisms causing inflammation due to a defective BBB could help to promote the use of anti-inflammatory therapies for age-related neurodegeneration. | Garcia, E. L., Steiner, R. E., Raimer, A. C., Herring, L. E., Matera, A. G., Spring, A. M. (2024). Dysregulation of innate immune signaling in animal models of spinal muscular atrophy. BMC Biol, 22(1):94 PubMed ID: 38664795
Summary: Spinal muscular atrophy (SMA) is a devastating neuromuscular disease caused by hypomorphic loss of function in the survival motor neuron (SMN) protein. SMA presents across a broad spectrum of disease severity. Unfortunately, genetic models of intermediate SMA have been difficult to generate in vertebrates and are thus unable to address key aspects of disease etiology. To address these issues, we developed a Drosophila model system that recapitulates the full range of SMA severity, allowing studies of pre-onset biology as well as late-stage disease processes. Transcriptomic and proteomic profiling was carried out of mild and intermediate Drosophila models of SMA to elucidate molecules and pathways that contribute to the disease. Using this approach, a role was elaborated for the SMN complex in the regulation of innate immune signaling. Mutation or tissue-specific depletion of SMN induces hyperactivation of the immune deficiency (IMD) and Toll pathways, leading to overexpression of antimicrobial peptides (AMPs) and ectopic formation of melanotic masses in the absence of an external challenge. Furthermore, the knockdown of downstream targets of these signaling pathways reduced melanotic mass formation caused by SMN loss. Importantly, SMN was identified as a negative regulator of a ubiquitylation complex that includes Traf6, Bendless, and Diap2 and plays a pivotal role in several signaling networks. In alignment with recent research on other neurodegenerative diseases, these findings suggest that hyperactivation of innate immunity contributes to SMA pathology. This work not only provides compelling evidence that hyperactive innate immune signaling is a primary effect of SMN depletion, but it also suggests that the SMN complex plays a regulatory role in this process in vivo. In summary, immune dysfunction in SMA is a consequence of reduced SMN levels and is driven by cellular and molecular mechanisms that are conserved between insects and mammals. |
| Yuan, Y., Yu, L., Zhuang, X., Wen, D., He, J., Hong, J., Xie, J., Ling, S., Du, X., Chen, W., Wang, X. (2025). Drosophila models used to simulate human ATP1A1 gene mutations that cause Charcot-Marie-Tooth type 2 disease and refractory seizures. Neural Regen Res, 20(1):265-276 PubMed ID: 38767491
Summary: Certain amino acids changes in the human Na+/K+-ATPase pump, ATPase Na+/K+ transporting subunit alpha 1 (ATP1A1), cause Charcot-Marie-Tooth disease type 2 (CMT2) disease and refractory seizures. To develop in vivo models to study the role of Na+/K+-ATPase in these diseases, the Drosophila gene homolog, Atpα, was modified to mimic the human ATP1A1 gene mutations that cause CMT2. Mutations located within the helical linker region of human ATP1A1 (I592T, A597T, P600T, and D601F) were simultaneously introduced into endogenous Drosophila Atpα by CRISPR/Cas9-mediated genome editing, generating the AtpαTTTF model. In addition, the same strategy was used to generate the corresponding single point mutations in flies (AtpαI571T, AtpαA576T, AtpαP579T, and AtpαD580F). Moreover, a deletion mutation (Atpαmut) that causes premature termination of translation was generated as a positive control. Of these alleles, two were found that could be maintained as homozygotes (AtpαI571T and AtpαP579T). Three alleles (AtpαA576T, AtpαP579 and AtpαD580F) can form heterozygotes with the Atpαmut allele. The Atpα allele carrying these CMT2-associated mutations showed differential phenotypes in Drosophila. Flies heterozygous for AtpαTTTF mutations have motor performance defects, a reduced lifespan, seizures, and an abnormal neuronal morphology. These Drosophila models will provide a new platform for studying the function and regulation of the sodium-potassium pump. | Lobato, A. G., Ortiz-Vega, N., Zhu, Y., Neupane, D., Meier, K. K., Zhai, R. G. (2024). Copper enhances aggregational toxicity of mutant huntingtin in a Drosophila model of Huntington's Disease. Biochimica et biophysica acta Molecular basis of disease, 1870(1):166928 PubMed ID: 38660915
Summary: Huntington's disease (HD) is a progressive neurodegenerative disorder with clinical presentations of moderate to severe cognitive, motor, and psychiatric disturbances. HD is caused by the trinucleotide repeat expansion of CAG of the huntingtin (HTT) gene. The mutant HTT protein containing pathological polyglutamine (polyQ) extension is prone to misfolding and aggregation in the brain. It has previously been observed that copper and iron concentrations are increased in the striata of post-mortem human HD brains. Although it has been shown that the accumulation of mutant HTT protein can interact with copper, the underlying HD progressive phenotypes due to copper overload remains elusive. Here, in a Drosophila model of HD, this study showed that copper induces dose-dependent aggregational toxicity and enhancement of Htt-induced neurodegeneration. Specifically, copper was found to increase mutant Htt aggregation, enhance the accumulation of Thioflavin S positive β-amyloid structures within Htt aggregates, and consequently alter autophagy in the brain. Administration of copper chelator D-penicillamine (DPA) through feeding significantly decreases β-amyloid aggregates in the HD pathological model. These findings reveal a direct role of copper in potentiating mutant Htt protein-induced aggregational toxicity, and further indicate the potential impact of environmental copper exposure in the disease onset and progression of HD. |
| Melkani, Y., Pant, A., Guo, Y., Melkani, G. C. (2024). Automated assessment of cardiac dynamics in aging and dilated cardiomyopathy Drosophila models using machine learning. Communications biology, 7(1):702 PubMed ID: 38849449
Summary: Drosophila model is pivotal in deciphering the pathophysiological underpinnings of various human ailments, notably aging and cardiovascular diseases. Cutting-edge imaging techniques and physiology yield vast high-resolution videos, demanding advanced analysis methods. This platform leverages deep learning to segment optical microscopy images of Drosophila hearts, enabling the quantification of cardiac parameters in aging and dilated cardiomyopathy (DCM). Validation using experimental datasets confirms the efficacy of this aging model. Two innovative approaches, deep-learning video classification and machine-learning based on cardiac parameters were used to predict fly aging, achieving accuracies of 83.3% (AUC 0.90) and 79.1%, (AUC 0.87) respectively. Moreover, deep-learning methodology was extended to assess cardiac dysfunction associated with the knock-down of oxoglutarate dehydrogenase (OGDH), revealing its potential in studying DCM. This versatile approach promises accelerated cardiac assays for modeling various human diseases in Drosophila and holds promise for application in animal and human cardiac physiology under diverse conditions. | Ho, D. M., Shaban, M., Mahmood, F., Ganguly, P., Todeschini, L., Van Vactor, D., Artavanis-Tsakonas, S. (2024). cAMP/PKA signaling regulates TDP-43 aggregation and mislocalization. Proc Natl Acad Sci U S A, 121(24):e2400732121 PubMed ID: 38838021
Summary: Cytoplasmic mislocalization and aggregation of TDP-43 protein are hallmarks of amyotrophic lateral sclerosis (ALS) and are observed in the vast majority of both familial and sporadic cases. How these two interconnected processes are regulated on a molecular level, however, remains enigmatic. Genome-wide screens for modifiers of the ALS-associated genes TDP-43 and FUS have identified the phospholipase D (Pld) pathway as a key regulator of ALS-related phenotypes in the fruit fly Drosophila melanogaster [M. W. Kankel et al., Genetics 215, 747-766 (2020)]. This study reports the results of a search for downstream targets of the enzymatic product of Pld, phosphatidic acid. Two conserved negative regulators of the cAMP/PKA signaling pathway, the phosphodiesterase dunce and the inhibitory subunit PKA-R2, as modifiers of pathogenic phenotypes resulting from overexpression of the Drosophila TDP-43 ortholog TBPH. Knockdown of either of these genes results in a mitigation of both TBPH aggregation and mislocalization in larval motor neuron cell bodies, as well as an amelioration of adult-onset motor defects and shortened lifespan induced by TBPH. PKA kinase activity is downstream of both TBPH and Pld, and overexpression of the PKA target CrebA can rescue TBPH mislocalization. These findings suggest a model whereby increasing cAMP/PKA signaling can ameliorate the molecular and functional effects of pathological TDP-43. |
Wednesday, February 19th - Larval and Adult Neural Structure, Development and Function |
| Luedke, K. P., Yoshino, J., Yin, C., Jiang, N., Huang, J. M., Huynh, K., Parrish, J. Z. (2024). Dendrite intercalation between epidermal cells tunes nociceptor sensitivity to mechanical stimuli in Drosophila larvae. PLoS Genet, 20(4):e1011237 PubMed ID: 38662763
Summary: An animal's skin provides a first point of contact with the sensory environment, including noxious cues that elicit protective behavioral responses. Nociceptive somatosensory neurons densely innervate and intimately interact with epidermal cells to receive these cues, however the mechanisms by which epidermal interactions shape processing of noxious inputs is still poorly understood. This study identified a role for dendrite intercalation between epidermal cells in tuning sensitivity of Drosophila larvae to noxious mechanical stimuli. In wild-type larvae, dendrites of nociceptive class IV da neurons intercalate between epidermal cells at apodemes, which function as body wall muscle attachment sites, but not at other sites in the epidermis. From a genetic screen >miR-14 was identified as a regulator of dendrite positioning in the epidermis: >miR-14 is expressed broadly in the epidermis but not in apodemes, and >miR-14inactivation leads to excessive apical dendrite intercalation between epidermal cells. >miR-14 was found to regulate expression and distribution of the epidermal Innexins ogre and Inx2 and that these epidermal gap junction proteins restrict epidermal dendrite intercalation. Finally, altering the extent of epidermal dendrite intercalation had corresponding effects on nociception: increasing epidermal intercalation sensitized larvae to noxious mechanical inputs and increased mechanically evoked calcium responses in nociceptive neurons, whereas reducing epidermal dendrite intercalation had the opposite effects. Altogether, these studies identify epidermal dendrite intercalation as a mechanism for mechanical coupling of nociceptive neurons to the epidermis, with nociceptive sensitivity tuned by the extent of intercalation. | Yoshikawa, S., Tang, P., Simpson, J. H. (2024). Mechanosensory and command contributions to the Drosophila grooming sequence. Curr Biol, 34(10):2066-2076. PubMed ID: 38657610
Summary: Flies groom in response to competing mechanosensory cues in an anterior-to-posterior order using specific legs. From behavior screens, a pair of cholinergic command-like neurons, Mago-no-Te (MGT) were identified, whose optogenetic activation elicits thoracic grooming by the back legs. Thoracic grooming is typically composed of body sweeps and leg rubs in alternation, but clonal analysis coupled with amputation experiments revealed that MGT activation only commands the body sweeps: initiation of leg rubbing requires contact between the leg and thorax. With new electron microscopy (EM) connectome data for the ventral nerve cord (VNC)<>, a circuit-based explanation was uncovered for why stimulation of posterior thoracic mechanosensory bristles initiates cleaning by the back legs. Previous work showed that flies weigh mechanosensory inputs across the body to select which part to groom, but it was not know why the thorax was always cleaned last. The connectome for the VNC enabled identification of a pair of GABAergic inhibitory neurons, UMGT1, that receives diverse sensory inputs and synapses onto both MGT and components of its downstream circuits. Optogenetic activation of UMGT1 suppresses thoracic cleaning, representing a mechanism by which mechanosensory stimuli on other body parts could take precedence in the grooming hierarchy. The pre-motor circuit downstream of MGT was anatomically mapped, including inhibitory feedback connections that may enable rhythmicity and coordination of limb movement during thoracic grooming. The combination of behavioral screens and connectome analysis allowed identification a neural circuit connecting sensory-to-motor neurons that contributes to thoracic grooming. |
| Nern, A., Loesche, F., Takemura, S. Y., Burnett, L. E., Dreher, M.,..., Berg, S., Rubin, G. M., Reiser, M. B. (2024). Connectome-driven neural inventory of a complete visual system.. bioRxiv, PubMed ID: 38659887
Summary: Vision provides animals with detailed information about their surroundings, conveying diverse features such as color, form, and movement across the visual scene. Computing these parallel spatial features requires a large and diverse network of neurons, such that in animals as distant as flies and humans, visual regions comprise half the brain's volume. These visual brain regions often reveal remarkable structure-function relationships, with neurons organized along spatial maps with shapes that directly relate to their roles in visual processing. To unravel the stunning diversity of a complex visual system, a careful mapping of the neural architecture matched to tools for targeted exploration of that circuitry is essential. This study reports a new connectome of the right optic lobe from a male Drosophila central nervous system FIB-SEM volume and a comprehensive inventory of the fly's visual neurons. A computational framework was developed to quantify the anatomy of visual neurons, establishing a basis for interpreting how their shapes relate to spatial vision. By integrating this analysis with connectivity information, neurotransmitter identity, and expert curation, ~53,000 neurons were classified into 727 types, about half of which are systematically described and named for the first time. Finally, an extensive collection of split-GAL4 lines matched to the neuron type catalog is shared. Together, this comprehensive set of tools and data unlock new possibilities for systematic investigations of vision in Drosophila, a foundation for a deeper understanding of sensory processing. | Desai, M., Hemant, Deo, A., Naik, J., Dhamale, P., Kshirsagar, A., Bose, T., Majumdar, A. (2024). Mrj is a chaperone of the Hsp40 family that regulates Orb2 oligomerization and long-term memory in Drosophila. PLoS Biol, 22(4):e3002585 PubMed ID: 38648719
Summary: Orb2 the Drosophila homolog of cytoplasmic polyadenylation element binding (CPEB) protein forms prion-like oligomers. These oligomers consist of Orb2A and Orb2B isoforms and their formation is dependent on the oligomerization of the Orb2A isoform. Drosophila with a mutation diminishing Orb2A's prion-like oligomerization forms long-term memory but fails to maintain it over time. Since this prion-like oligomerization of Orb2A plays a crucial role in the maintenance of memory, this study aimed to find what regulates this oligomerization. In an immunoprecipitation-based screen, interactors of Orb2A were identified in the Hsp40 and Hsp70 families of proteins. Among these, an Hsp40 family protein Mrj was identified as a regulator of the conversion of Orb2A to its prion-like form. Mrj interacts with Hsp70 proteins and acts as a chaperone by interfering with the aggregation of pathogenic Huntingtin. Unlike its mammalian homolog, Drosophila Mrj was identified is neither an essential gene nor causes any gross neurodevelopmental defect. A loss of Mrj results in a reduction in Orb2 oligomers. Further, Mrj knockout exhibits a deficit in long-term memory and our observations suggest Mrj is needed in mushroom body neurons for the regulation of long-term memory. This work implicates a chaperone Mrj in mechanisms of memory regulation through controlling the oligomerization of Orb2A and its association with the translating ribosomes. |
| Zhuravlev, A. V., Vetrovoy, O. V., Zalomaeva, E. S., Egozova, E. S., Nikitina, E. A., Savvateeva-Popova, E. V. (2024). Overexpression of the limk1 Gene in Drosophila melanogaster Can Lead to Suppression of Courtship Memory in Males. Biochemistry (Mosc), 89(3):393-406 PubMed ID: 38648760
Summary: Courtship suppression is a behavioral adaptation of the fruit fly. When majority of the females in a fly population are fertilized and non-receptive for mating, a male, after a series of failed attempts, decreases its courtship activity towards all females, saving its energy and reproductive resources. The time of courtship decrease depends on both duration of unsuccessful courtship and genetically determined features of the male nervous system. Thereby, courtship suppression paradigm can be used for studying molecular mechanisms of learning and memory. phosoph-Cofilin, a component of the actin remodeling signaling cascade and product of LIM-kinase 1 (LIMK1), regulates Drosophila melanogaster forgetting in olfactory learning paradigm. Previous, work has shown that Limk1 suppression in the specific types of nervous cells differently affects fly courtship memory. This study used Gal4 > UAS system to induce limk1 overexpression in the same types of neurons. limk1 activation in the mushroom body, glia, and fruitless neurons decreased learning index compared to the control strain or the strain with limk1 knockdown. In cholinergic and dopaminergic/serotoninergic neurons, both overexpression and knockdown of limk1 impaired Drosophila short-term memory. Thus, proper balance of the limk1 activity is crucial for normal cognitive activity of the fruit fly. | Tran, H., Le, L., Singh, B. N., Kramer, J., Steward, R. (2024). Tet controls axon guidance in early brain development through glutamatergic signaling. iScience, 27(5):109634 PubMed ID: 38655199
Summary: Mutations in ten-eleven translocation (TET) proteins are associated with human neurodevelopmental disorders. This study found a function of Tet in regulating Drosophila early brain development. The Tet DNA-binding domain (Tet(AXXC)) is required for axon guidance in the mushroom body (MB). Glutamine synthetase 2 (Gs2), a key enzyme in glutamatergic signaling, is significantly down-regulated in the Tet(AXXC) brains. Loss of Gs2 recapitulates the Tet(AXXC) phenotype. Surprisingly, Tet and Gs2 act in the insulin-producing cells (IPCs) to control MB axon guidance, and overexpression of Gs2 in IPCs rescues the defects of Tet(AXXC). Feeding Tet(AXXC) with metabotropic glutamate receptor antagonist MPEP rescues the phenotype while glutamate enhances it. Mutants in Tet and Drosophila Fmr1, the homolog of human FMR1, have similar defects, and overexpression of Gs2 in IPCs also rescues the Fmr1 phenotype. This study provides the first evidence that Tet controls the guidance of developing brain axons by modulating glutamatergic signaling. |
Tuesday, February 18th - Embryonic Development |
| Wang, Z., Lin, X., Shi, W., Cao, C. (2024). Nicotinic Acetylcholine Receptor Alpha6 Contributes to Antiviral Immunity via IMD Pathway in Drosophila melanogaster. Viruses, 16(4) PubMed ID: 38675904
Summary: Currently, insecticides that target nicotinic acetylcholine receptors (nAChR) are widely used. Studies on the sublethal effects of insecticides have found that they can affect the amount of virus in insects. The mechanism by which insecticides affect insect virus load remain unclear. Here, we show that nAChR targeting insecticide can affect viral replication through the immune deficiency (IMD) pathway. We demonstrate that a low dose of spinosad (6.8 ng/mL), acting as an antagonist to Drosophila melanogaster nicotinic acetylcholine receptor α6 (Dα6), significantly elevates Drosophila melanogaster sigmavirus (DMelSV) virus titers in adults of Drosophila melanogaster. Conversely, a high dose of spinosad (50 ng/mL), acting as an agonist to Dα6, substantially decreases viral load. This bidirectional regulation of virus levels is absent in Dα6-knockout flies, signifying the specificity of spinosad's action through Dα6. Furthermore, the knockdown of Dα6 results in decreased expression of genes in the IMD pathway, including dredd, imd, relish, and downstream antimicrobial peptide genes AttA and AttB, indicating a reduced innate immune response. Subsequent investigations reveal no significant difference in viral titers between relish mutant flies and Dα6-relish double mutants, suggesting that the IMD pathway's role in antiviral defense is dependent on Dα6. Collectively, these findings shed light on the intricate interplay between nAChR signaling and the IMD pathway in mediating antiviral immunity, highlighting the potential for nAChR-targeting compounds to inadvertently influence viral dynamics in insect hosts. This knowledge may inform the development of integrated pest management strategies that consider the broader ecological impact of insecticide use. | Ruan, Z. R., Yu, Z., Xing, C., Chen, E. H. (2024). Inter-organ steroid hormone signaling promotes myoblast fusion via direct transcriptional regulation of a single key effector gene. Curr Biol, 34(7):1438-1452.e1436 PubMed ID: 38513654
Summary: Steroid hormones regulate tissue development and physiology by modulating the transcription of a broad spectrum of genes. In insects, the principal steroid hormones, ecdysteroids, trigger the expression of thousands of genes through a cascade of transcription factors (TFs) to coordinate developmental transitions such as larval molting and metamorphosis. However, whether ecdysteroid signaling can bypass transcriptional hierarchies to exert its function in individual developmental processes is unclear. This study reports that a single non-TF effector gene mediates the transcriptional output of ecdysteroid signaling in Drosophila myoblast fusion, a critical step in muscle development and differentiation. Specifically, we show that the 20-hydroxyecdysone (commonly referred to as "ecdysone") secreted from an extraembryonic tissue, amnioserosa, acts on embryonic muscle cells to directly activate the expression of antisocial (ants), which encodes an essential scaffold protein enriched at the fusogenic synapse. Not only is ants transcription directly regulated by the heterodimeric ecdysone receptor complex composed of ecdysone receptor (EcR) and ultraspiracle (USP) via ecdysone-response elements but also more strikingly, expression of ants alone is sufficient to rescue the myoblast fusion defect in ecdysone signaling-deficient mutants. EcR/USP and a muscle-specific TF Twist synergistically activate ants expression in vitro and in vivo. Taken together, this study provides the first example of a steroid hormone directly activating the expression of a single key non-TF effector gene to regulate a developmental process via inter-organ signaling and provides a new paradigm for understanding steroid hormone signaling in other developmental and physiological processes. |
| Komori, H., Rastogi, G., Bugay, J. P., Luo, H., Lin, S., Angers, S., Smibert, C. A., Lipshitz, H. D., Lee, C. Y. (2024). Post-transcriptional regulatory pre-complex assembly drives timely cell-state transitions during differentiation. bioRxiv, PubMed ID: 38746105
Summary: Complexes that control mRNA stability and translation promote timely cell-state transitions during differentiation by ensuring appropriate expression patterns of key developmental regulators. The Drosophila RNA-binding protein Brain tumor (Brat) promotes degradation of target transcripts during the maternal-to-zygotic transition in syncytial embryos and in uncommitted intermediate neural progenitors (immature INPs). Ubiquitin-specific protease 5 (Usp5)was identifed as a Brat interactor essential for the degradation of Brat target mRNAs in both cell types. Usp5 promotes Brat-dedadenylase pre-complex assembly in mitotic neural stem cells (neuroblasts) by bridging Brat and the scaffolding components of deadenylase complexes lacking their catalytic subunits. The adaptor protein Miranda binds the RNA-binding domain of Brat, limiting its ability to bind target mRNAs in mitotic neuroblasts. Cortical displacement of Miranda activates Brat-mediated mRNA decay in immature INPs. It is proposed that the assembly of an enzymatically inactive and RNA-binding-deficient pre-complex poises mRNA degradation machineries for rapid activation driving timely developmental transitions. | Loyer, N., Hogg, E. K. J., Shaw, H. G., Pasztor, A., Murray, D. H., Findlay, G. M., Januschke, J. (2024). A CDK1 phosphorylation site on Drosophila PAR-3 regulates neuroblast polarisation and sensory organ formation. Elife, 13 PubMed ID: 38869055
Summary: The generation of distinct cell fates during development depends on asymmetric cell division of progenitor cells. In the central and peripheral nervous system of Drosophila, progenitor cells respectively called neuroblasts or sensory organ precursors use PAR polarity during mitosis to control cell fate determination in their daughter cells. How polarity and the cell cycle are coupled, and how the cell cycle machinery regulates PAR protein function and cell fate determination is poorly understood. This study generated an analog sensitive allele of CDK1 and revealed that its partial inhibition weakens but does not abolish apical polarity in embryonic and larval neuroblasts and leads to defects in polarisation of fate determinants. A novel in vivo phosphorylation is described of Bazooka, the Drosophila homolog of PAR-3, on Serine180, a consensus CDK phosphorylation site. In some tissular contexts, phosphorylation of Serine180 occurs in asymmetrically dividing cells but not in their symmetrically dividing neighbours. In neuroblasts, Serine180 phosphomutants disrupt the timing of basal polarisation. Serine180 phosphomutants also affect the specification and binary cell fate determination of sensory organ precursors as well as Baz localisation during their asymmetric cell divisions. Finally, this study shows that CDK1 phosphorylates Serine-S180 and an equivalent Serine on human PAR-3 in vitro. |
| Gamblin, C. L., Alende, C., Corriveau, F., Jette, A., Parent-Prevost, F., Biehler, C., Majeau, N., Laurin, M., Laprise, P. (2024).. The polarity protein Yurt associates with the plasma membrane via basic and hydrophobic motifs embedded in its FERM domain. J Cell Sci, 137(10) PubMed ID: 38682269
Summary: The subcellular distribution of the polarity protein Yurt (Yrt) is subjected to a spatio-temporal regulation in Drosophila melanogaster embryonic epithelia. After cellularization, Yrt binds to the lateral membrane of ectodermal cells and maintains this localization throughout embryogenesis. During terminal differentiation of the epidermis, Yrt accumulates at septate junctions and is also recruited to the apical domain. Although the mechanisms through which Yrt associates with septate junctions and the apical domain have been deciphered, how Yrt binds to the lateral membrane remains as an outstanding puzzle. This study shows that the FERM domain of Yrt is necessary and sufficient for membrane localization. The data also establish that the FERM domain of Yrt directly binds negatively charged phospholipids. Moreover, it was demonstrated that positively charged amino acid motifs embedded within the FERM domain mediates Yrt membrane association. Finally, evidence is provided suggesting that Yrt membrane association is functionally important. Overall, this study highlights the molecular basis of how Yrt associates with the lateral membrane during the developmental time window where it is required for segregation of lateral and apical domains. | Lye, C. M., Blanchard, G. B., Evans, J., Nestor-Bergmann, A., Sanson, B. (2024). Polarised cell intercalation during Drosophila axis extension is robust to an orthogonal pull by the invaginating mesoderm. PLoS Biol, 22(4):e3002611 PubMed ID: 38683880
Summary: As tissues grow and change shape during animal development, they physically pull and push on each other, and these mechanical interactions can be important for morphogenesis. During Drosophila gastrulation, mesoderm invagination temporally overlaps with the convergence and extension of the ectodermal germband; the latter is caused primarily by Myosin II-driven polarised cell intercalation. This study investigated the impact of mesoderm invagination on ectoderm extension, examining possible mechanical and mechanotransductive effects on Myosin II recruitment and polarised cell intercalation. The germband ectoderm was found to be deformed by the mesoderm pulling in the orthogonal direction to germband extension (GBE), showing mechanical coupling between these tissues. However, no significant change was found in Myosin II planar polarisation in response to mesoderm invagination, nor in the rate of junction shrinkage leading to neighbour exchange events. It is concluded that the main cellular mechanism of axis extension, polarised cell intercalation, is robust to the mesoderm invagination pull. However, it was found that mesoderm invagination slows down the rate of anterior-posterior cell elongation that contributes to axis extension, counteracting the tension from the endoderm invagination, which pulls along the direction of GBE. |
Thursday, February 13th - Signaling |
| Duan, C. Y., Li, Y., Zhi, H. Y., Tian, Y., Huang, Z. Y., Chen, S. P., Zhang, Y., Liu, Q., Zhou, L., Jiang, X. G., Ullah, K., Guo, Q., Liu, Z. H., Xu, Y., Han, J. H., Hou, J., O'Connor, D. P., Xu, G. (2024). E3 ubiquitin ligase UBR5 modulates circadian rhythm by facilitating the ubiquitination and degradation of the key clock transcription factor BMAL1. Acta pharmacologica Sinica, 45(9):1793-1808 PubMed ID: 38740904
Summary: The circadian clock is the inner rhythm of life activities and is controlled by a self-sustained and endogenous molecular clock, which maintains a ~ 24 h internal oscillation. As the core element of the circadian clock, BMAL1 is susceptible to degradation through the ubiquitin-proteasome system (UPS). Nevertheless, scant information is available regarding the UPS enzymes that intricately modulate both the stability and transcriptional activity of BMAL1, affecting the cellular circadian rhythm. This work we identified and validated UBR5 as a new E3 ubiquitin ligase that interacts with BMAL1 by using affinity purification, mass spectrometry, and biochemical experiments. UBR5 overexpression induced BMAL1 ubiquitination, leading to diminished stability and reduced protein level of BMAL1, thereby attenuating its transcriptional activity. Consistent with this, UBR5 knockdown increases the BMAL1 protein. Domain mapping discloses that the C-terminus of BMAL1 interacts with the N-terminal domains of UBR5. Similarly, cell-line-based experiments discover that HYD, the UBR5 homolog in Drosophila, could interact with and downregulate CYCLE, the BMAL1 homolog in Drosophila. PER2-luciferase bioluminescence real-time reporting assay in a mammalian cell line and behavioral experiments in Drosophila reveal that UBR5 or hyd knockdown significantly reduces the period of the circadian clock. Therefore, this work discovers a new ubiquitin ligase UBR5 that regulates BMAL1 stability and circadian rhythm and elucidates the underlying molecular mechanism. This work provides an additional layer of complexity to the regulatory network of the circadian clock at the post-translational modification level, offering potential insights into the modulation of the dysregulated circadian rhythm. | Lee, J. E., Lee, H., Baek, E., Choi, B., Yun, H. S., Yoo, Y. K., Lee, Y. S., Song, G. J., Cho, K. S. (2024). The role of glial and neuronal Eph/ephrin signaling in Drosophila mushroom body development and sleep and circadian behavior. Biochem Biophys Res Commun, 720:150072 PubMed ID: 38749187
Summary: The Eph receptor, a prototypically large receptor protein tyrosine kinase, interacts with ephrin ligands, forming a bidirectional signaling system that impacts diverse brain functions. Eph receptors and ephrins mediate forward and reverse signaling, affecting neurogenesis, axon guidance, and synaptic signaling. While mammalian studies have emphasized their roles in neurogenesis and synaptic plasticity, the Drosophila counterparts are less studied, especially in glial cells, despite structural similarities. Using RNAi to modulate Eph/ephrin expression in Drosophila neurons and glia, their roles in brain development and sleep and circadian behavior were studied. Knockdown of neuronal ephrin disrupted mushroom body development, while glial knockdown had minimal impact. Surprisingly, disrupting ephrin in neurons or glial cells altered sleep and circadian rhythms, indicating a direct involvement in these behaviors independent from developmental effects. Further analysis revealed distinct sleep phenotypes between neuronal and glial knockdowns, underscoring the intricate interplay within the neural circuits that govern behavior. Glia-specific knockdowns showed altered sleep patterns and reduced circadian rhythmicity, suggesting an intricate role of glia in sleep regulation. These findings challenge simplistic models of Eph/ephrin signaling limited to neuron-glia communication and emphasize the complexity of the regulatory networks modulating behavior. Future investigations targeting specific glial subtypes will enhance understanding of Eph/ephrin signaling's role in sleep regulation across species. |
| Ehlers, S. F., Manikowski, D., Steffes, G., Ehring, K., Gude, F., Grobe, K. (2024). A Residual N-Terminal Peptide Enhances Signaling of Depalmitoylated Hedgehog to the Patched Receptor. Journal of developmental biology, 12(2) PubMed ID: 38651456
Summary: During their biosynthesis, Sonic hedgehog (Shh; see Drosophia Hedgehog) morphogens are covalently modified by cholesterol at the C-terminus and palmitate at the N-terminus. Although both lipids initially anchor Shh to the plasma membrane of producing cells, it later translocates to the extracellular compartment to direct developmental fates in cells expressing the Patched (Ptch) receptor. Possible release mechanisms for dually lipidated Hh/Shh into the extracellular compartment are currently under intense debate. This paper describeS the serum-dependent conversion of the dually lipidated cellular precursor into a soluble cholesteroylated variant (Shh(C)) during its release. Although Shh(C) is formed in a Dispatched- and Scube2-dependent manner, suggesting the physiological relevance of the protein, the depalmitoylation of Shh(C) during release is inconsistent with the previously postulated function of N-palmitate in Ptch receptor binding and signaling. Therefore, the potency of Shh(C) to induce Ptch-controlled target cell transcription and differentiation in Hh-sensitive reporter cells and in the Drosophila eye was examined. In both experimental systems, Shh(C) was highly bioactive despite the absence of the N-palmitate. The artificial removal of N-terminal peptides longer than eight amino acids inactivated the depalmitoylated soluble proteins in vitro and in the developing Drosophila eye. These results demonstrate that N-depalmitoylated Shh(C) requires an N-peptide of a defined minimum length for its signaling function to Ptch. | Pandey, A., Roy, J. K. (2024). Rab11 maintains the undifferentiated state of adult midgut precursors via DPP pathway. Exp Cell Res, 439(1):114092 PubMed ID: 38754617
Summary: Asymmetric stem cell divisions play instrumental roles in the maintenance, growth and differentiation of organs. Failure of asymmetric stem cell divisions may result in an array of developmental disorders, including cancer. It is well established that the gene, inscuteable, acts as the upstream component of asymmetric cell divisions. In Drosophila larval midgut, a founder adult midgut precursor (AMP) experiences an asymmetric division to instruct its first daughter to become a peripheral cell that serves as a niche where the AMP and its future daughters can remain undifferentiated. This study demonstrates that inscuteable expressing stem cells require Rab11, a conserved small Ras-like GTPase, for proper proliferation and differentiation. As insc-GAL4 mediated Rab11RNAi in Drosophila larval and adult midguts show the disruption of the niche microenvironment of adult midgut precursors as well as elevated DPP signalling at the larval stage, which is associated with aberrant over-proliferation and early differentiation of larval AMPs and adult intestinal stem cells. The observed connections between Rab11, larval AMP proliferation, niche establishment, and DPP signalling highlight the potential for Rab11 to serve as a key regulatory factor in maintaining tissue homeostasis and balanced cellular growth. |
| Verma, D., Singh, A., Singh, J., Mutsuddi, M., Mukherjee, A. (2024). Regulation of Notch signaling by non-muscle myosin II Zipper in Drosophila. Cell Mol Life Sci, 81(1):195 PubMed ID: 38653877
Summary: The Notch pathway is an evolutionarily conserved signaling system that is intricately regulated at multiple levels and it influences different aspects of development. In an effort to identify novel components involved in Notch signaling and its regulation, protein interaction screens were carried out thath identified non-muscle myosin II Zipper (Zip) as an interacting partner of Notch. Physical interaction between Notch and Zip was further validated by co-immunoprecipitation studies. Immunocytochemical analyses revealed that Notch and Zip co-localize within same cytoplasmic compartment. Different alleles of zip also showed strong genetic interactions with Notch pathway components. Downregulation of Zip resulted in wing phenotypes that were reminiscent of Notch loss-of-function phenotypes and a perturbed expression of Notch downstream targets, Cut and Deadpan. Further, synergistic interaction between Notch and Zip resulted in highly ectopic expression of these Notch targets. Activated Notch-induced tumorous phenotype of larval tissues was enhanced by over-expression of Zip. Notch-Zip synergy resulted in the activation of JNK pathway that consequently lead to MMP activation and proliferation. Taken together, these results suggest that Zip may play an important role in regulation of Notch signaling. | Sui, L., Dahmann, C. (2024). A cellular tilting mechanism important for dynamic tissue shape changes and cell differentiation in Drosophila. Dev Cell, 59(14):1794-1808.e1795 PubMed ID: 38692272
Summary: Dynamic changes in three-dimensional cell shape are important for tissue form and function. In the developing Drosophila eye, photoreceptor differentiation requires the progression across the tissue of an epithelial fold known as the morphogenetic furrow. Morphogenetic furrow progression involves apical cell constriction and movement of apical cell edges. This study shows that cells progressing through the morphogenetic furrow move their basal edges in opposite direction to their apical edges, resulting in a cellular tilting movement. Cells generate, at their basal side, oriented, force-generating protrusions. Knockdown of the protein kinase Src42A or photoactivation of a dominant-negative form of the small GTPase Rac1 reduces protrusion formation. Impaired protrusion formation stalls basal cell movement and slows down morphogenetic furrow progression and photoreceptor differentiation. This work identifies a cellular tilting mechanism important for the generation of dynamic tissue shape changes and cell differentiation. |
Wednesday, February 12th - Chromatin |
| Yuan, Y., Chen, Q., Brovkina, M., Clowney, E. J., Yadlapalli, S. (2024). Clock-dependent chromatin accessibility rhythms regulate circadian transcription. PLoS Genet, 20(5):e1011278 PubMed ID: 38805552
Summary: Chromatin organization plays a crucial role in gene regulation by controlling the accessibility of DNA to transcription machinery. While significant progress has been made in understanding the regulatory role of clock proteins in circadian rhythms, how chromatin organization affects circadian rhythms remains poorly understood. This study employed ATAC-seq (Assay for Transposase-Accessible Chromatin with Sequencing) on FAC-sorted Drosophila clock neurons to assess genome-wide chromatin accessibility at dawn and dusk over the circadian cycle. Significant oscillations were observed in chromatin accessibility at promoter and enhancer regions of hundreds of genes, with enhanced accessibility either at dusk or dawn, which correlated with their peak transcriptional activity. Notably, genes with enhanced accessibility at dusk were enriched with E-box motifs, while those more accessible at dawn were enriched with VRI/PDP1-box motifs, indicating that they are regulated by the core circadian feedback loops, PER/CLK and VRI/PDP1, respectively. Further, we observed a complete loss of chromatin accessibility rhythms in per01 null mutants, with chromatin consistently accessible at both dawn and dusk, underscoring the critical role of Period protein in driving chromatin compaction during the repression phase at dawn. Together, this study demonstrates the significant role of chromatin organization in circadian regulation, revealing how the interplay between clock proteins and chromatin structure orchestrates the precise timing of biological processes throughout the day. This work further implies that variations in chromatin accessibility might play a central role in the generation of diverse circadian gene expression patterns in clock neurons. | Narbey, R., Mouchel-Vielh, E., Gibert, J. M. (2024). The H3K79me3 methyl-transferase Grappa is involved in the establishment and thermal plasticity of abdominal pigmentation in Drosophila melanogaster females. Sci Rep, 14(1):9547 PubMed ID: 38664546
Summary: Temperature sensitivity of abdominal pigmentation in Drosophila melanogaster females allows to investigate the mechanisms underlying phenotypic plasticity. Thermal plasticity of pigmentation is due to modulation of tan and yellow expression, encoding pigmentation enzymes. Furthermore, modulation of tan expression by temperature is correlated to the variation of the active histone mark H3K4me3 on its promoter. This study tested the role of the DotCom complex, which methylates H3K79, another active mark, in establishment and plasticity of pigmentation. Several components of the DotCom complex are involved in the establishment of abdominal pigmentation. In particular, Grappa, the catalytic unit of this complex, plays opposite roles on pigmentation at distinct developmental stages. Indeed, its down-regulation from larval L2 to L3 stages increases female adult pigmentation, whereas its down-regulation during the second half of the pupal stage decreases adult pigmentation. These opposite effects are correlated to the regulation of distinct pigmentation genes by Grappa: yellow repression for the early role and tan activation for the late one. Lastly, reaction norms measuring pigmentation along temperature in mutants for subunits of the DotCom complex reveal that this complex is not only involved in the establishment of female abdominal pigmentation but also in its plasticity. |
| Bujosa, P., Reina, O., Caballé, A., Casas-Lamesa, A., Torras-Llort, M., Pérez-Roldán, J., Nacht, A. S., Vicent, G. P., Bernués, J., Azorin, F. (2024). Linker histone H1 regulates homeostasis of heterochromatin-associated cRNAs. Cell Rep, 43(5):114137 PubMed ID: 38662543
Summary: Chromatin-associated RNAs (cRNAs) are a poorly characterized fraction of cellular RNAs that co-purify with chromatin. Their full complexity and the mechanisms regulating their packaging and chromatin association remain poorly understood. This study addresses these questions in Drosophila. cRNAs were found to constitute a heterogeneous group of RNA species that is abundant in heterochromatic transcripts. Heterochromatic cRNAs were shown to interact with the heterogeneous nuclear ribonucleoproteins (hnRNP) hrp36/hrp48 and that depletion of linker histone dH1 impairs this interaction. dH1 depletion induces the accumulation of RNA::DNA hybrids (R-loops) in heterochromatin and, as a consequence, increases retention of heterochromatic cRNAs. These effects correlate with increased RNA polymerase II (RNAPII) occupancy at heterochromatin. Notably, impairing cRNA assembly by depletion of hrp36/hrp48 mimics heterochromatic R-loop accumulation induced by dH1 depletion. dH1 depletion was shown to alters nucleosome organization, increasing accessibility of heterochromatin. Altogether, these perturbations facilitate annealing of cRNAs to the DNA template, enhancing R-loop formation and cRNA retention at heterochromatin. | Snedeker, J., Davis, B. E. M., Ranjan, R., Wooten, M., Blundon, J., Chen, X. (2024). Reduced Levels of Lagging Strand Polymerases Shape Stem Cell Chromatin. bioRxiv, PubMed ID: 38746451
Summary: Stem cells display asymmetric histone inheritance while non-stem progenitor cells exhibit symmetric patterns in the Drosophila male germline lineage. This study reports that involved in lagging strand synthesis, such as Polδ), have significantly reduced levels in stem cells compared to progenitor cells. Compromising Polα genetically induces the replication-coupled histone incorporation pattern in progenitor cells to be indistinguishable from that in stem cells, which can be recapitulated using a Polα inhibitor in a concentration-dependent manner. Furthermore, stem cell-derived chromatin fibers display a higher degree of old histone recycling by the leading strand compared to progenitor cell-derived chromatin fibers. However, upon reducing Polα levels in progenitor cells, the chromatin fibers now display asymmetric old histone recycling just like GSC-derived fibers. The old versus new histone asymmetry is comparable between stem cells and progenitor cells at both S-phase and M-phase. Together, these results indicate that developmentally programmed expression of key DNA replication components is important to shape stem cell chromatin. Furthermore, manipulating one crucial DNA replication component can induce replication-coupled histone dynamics in non-stem cells in a manner similar to that in stem cells. |
| Brown, J. L., Zhang, L., Rocha, P. P., Kassis, J. A., Sun, M. A. (2024). Polycomb protein binding and looping in the ON transcriptional state.. Sci Adv, 10(17):eadn1837 PubMed ID: 38657072
Summary: Polycomb group (PcG) proteins mediate epigenetic silencing of important developmental genes by modifying histones and compacting chromatin through two major protein complexes, PRC1 and PRC2. These complexes are recruited to DNA by CpG islands (CGIs) in mammals and Polycomb response elements (PREs) in Drosophila. When PcG target genes are turned OFF, PcG proteins bind to PREs or CGIs, and PREs serve as anchors that loop together and stabilize gene silencing. This study addresses which PcG proteins bind to PREs and whether PREs mediate looping when their targets are in the ON transcriptional state. While the binding of most PcG proteins decreases at PREs in the ON state, one PRC1 component, Ph, remains bound. Further, PREs can loop to each other and with presumptive enhancers in the ON state and, like CGIs, may act as tethering elements between promoters and enhancers. Overall, these data suggest that PREs are important looping elements for developmental loci in both the ON and OFF states. | Vizjak, P., Kamp, D., Hepp, N., Scacchetti, A., Gonzalez Pisfil, M., Bartho, J., Halic, M., Becker, P. B., Smolle, M., Stigler, J., Mueller-Planitz, F. (2024). ISWI catalyzes nucleosome sliding in condensed nucleosome arrays. Nat Struct Mol Biol, PubMed ID: 38664566
Summary: How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. This study investigated these challenges using the Drosophila ISWi, which slides nucleosomes along DNA. Folding of chromatin fibers did not affect sliding in vitro. Catalytic rates were also comparable in- and outside of chromatin condensates. ISWI cross-links and thereby stiffens condensates, except when ATP hydrolysis is possible. Active hydrolysis is also required for ISWI's mobility in condensates. Energy from ATP hydrolysis therefore fuels ISWI's diffusion through chromatin and prevents ISWI from cross-linking chromatin. Molecular dynamics simulations of a 'monkey-bar' model in which ISWI grabs onto neighboring nucleosomes, then withdraws from one before rebinding another in an ATP hydrolysis-dependent manner, qualitatively agree with the data. Monkey-bar mechanisms could be shared with other chromatin factors and changes in chromatin dynamics caused by mutations in remodelers could contribute to pathologies. |
Tuesday, February 11th - Genes, Gene Families, and Proteins |
| Bereda, C. C., Dewey, E. B., Nasr, M. A., Sekelsky, J. (2024). Functions of the Bloom Syndrome Helicase N-terminal Intrinsically Disordered Region. bioRxiv, PubMed ID: 38659896
Summary: Bloom Syndrome helicase (Blm) is a RecQ family helicase involved in DNA repair, cell-cycle progression, and development. Pathogenic variants in human BLM cause the autosomal recessive disorder Bloom Syndrome, characterized by predisposition to numerous types of cancer. Prior studies of Drosophila Blm mutants lacking helicase activity or protein have shown sensitivity to DNA damaging agents, defects in repairing DNA double-strand breaks (DSBs), female sterility, and improper segregation of chromosomes in meiosis. Blm orthologs have a well conserved and highly structured RecQ helicase domain, but more than half of the protein, particularly in the N-terminus, is predicted to be unstructured. Because this region is poorly conserved across multicellular organisms, this study compared closely related species to identify regions of conservation, potentially indicating important functions. Two of these Drosophila-conserved regions were deleted nin D. melanogaster using CRISPR/Cas9 gene editing and assessed the effects on different Blm functions. Each deletion had distinct effects on different Blm activities. Deletion of either conserved region 1 (CR1) or conserved region 2 (CR2) compromised DSB repair through synthesis-dependent strand annealing and resulted in increased mitotic crossovers. In contrast, CR2 is critical for embryonic development but CR1 is not as important. CR1 deletion allows for proficient meiotic chromosome segregation but does lead to defects in meiotic crossover designation and patterning. Finally, deletion of CR2 does not lead to significant meiotic defects, indicating that while each region has overlapping functions, there are discreet roles facilitated by each. These results provide novel insights into functions of the N-terminal disordered region of Blm. | Watase, G. J., Yamashita, Y. M. (2024). DNA polymerase II-mediated rDNA transcription mediates rDNA copy number expansion in Drosophila. PLoS Genet, 20(5):e1011136 PubMed ID: 38758955
Summary: Ribosomal DNA (rDNA), which encodes ribosomal RNA, is an essential but unstable genomic element due to its tandemly repeated nature. rDNA's repetitive nature causes spontaneous intrachromatid recombination, leading to copy number (CN) reduction, which must be counteracted by a mechanism that recovers CN to sustain cells' viability. Akin to telomere maintenance, rDNA maintenance is particularly important in cell types that proliferate for an extended time period, most notably in the germline that passes the genome through generations. In Drosophila, the process of rDNA CN recovery, known as 'rDNA magnification', has been studied extensively. rDNA magnification is mediated by unequal sister chromatid exchange (USCE), which generates a sister chromatid that gains the rDNA CN by stealing copies from its sister. However, much remains elusive regarding how germ cells sense rDNA CN to decide when to initiate magnification, and how germ cells balance between the need to generate DNA double-strand breaks (DSBs) to trigger USCE vs. avoiding harmful DSBs. Recently, an rDNA-binding Zinc-finger protein Indra was identified as a factor required for rDNA magnification, however, the underlying mechanism of action remains unknown. This study shows that Indra is a negative regulator of rDNA magnification, balancing the need of rDNA magnification and repression of dangerous DSBs. Mechanistically, Indra was shown to be a repressor of RNA polymerase II (Pol II)-dependent transcription of rDNA: Under low rDNA CN conditions, Indra protein amount is downregulated, leading to Pol II-mediated transcription of rDNA. This results in the expression of rDNA-specific retrotransposon, R2, which facilitates rDNA magnification via generation of DBSs at rDNA. It is proposed that differential use of Pol I and Pol II plays a critical role in regulating rDNA CN expansion only when it is necessary. |
| Camp, D., Venkatesh, B., Solianova, V., Varela, L., Goult, B. T., Tanentzapf, G. (2024). The actin binding sites of talin have both distinct and complementary roles in cell-ECM adhesion. PLoS Genet, 20(4):e1011224 PubMed ID: 38662776
Summary: Cell adhesion requires linkage of transmembrane receptors to the cytoskeleton through intermediary linker proteins. Integrin-based adhesion to the extracellular matrix (ECM) involves large adhesion complexes that contain multiple cytoskeletal adapters that connect to the actin cytoskeleton. Many of these adapters, including the essential cytoskeletal linker Talin, have been shown to contain multiple actin-binding sites (ABSs) within a single protein. To investigate the possible role of having such a variety of ways of linking integrins (see Myospheroid) to the cytoskeleton, mutations were generated in multiple actin binding sites in Drosophila talin. Using this approach, different actin-binding sites in talin were shown to have both unique and complementary roles in integrin-mediated adhesion. Specifically, mutations in either the C-terminal ABS3 or the centrally located ABS2 result in lethality showing that they have unique and non-redundant function in some contexts. On the other hand, flies simultaneously expressing both the ABS2 and ABS3 mutants exhibit a milder phenotype than either mutant by itself, suggesting overlap in function in other contexts. Detailed phenotypic analysis of ABS mutants elucidated the unique roles of the talin ABSs during embryonic development as well as provided support for the hypothesis that talin acts as a dimer in in vivo contexts. | Park, K., Choi, H., Han, I. J., Asefa, W. R., Jeong, C., Yu, S., Jeong, H., Choi, M., Yoon, S. E., Kim, Y. J., Choi, M. S., Kwon, J. Y. (2024). Molecular and cellular organization of odorant binding protein genes in Drosophila.. Heliyon, 10(9):e29358 PubMed ID: 38694054
Summary: Chemosensation is important for the survival and reproduction of animals. The odorant binding proteins (OBPs) are thought to be involved in chemosensation together with chemosensory receptors. While OBPs were initially considered to deliver hydrophobic odorants to olfactory receptors in the aqueous lymph solution, recent studies suggest more complex roles in various organs. This study used GAL4 transgenes to systematically analyze the expression patterns of all 52 members of the Obp gene family and 3 related chemosensory protein genes in adult Drosophila, focusing on chemosensory organs such as the antenna, maxillary palp, pharynx, and labellum, and other organs such as the brain, ventral nerve cord, leg, wing, and intestine. The OBPs were observed to express in diverse organs and in multiple cell types, suggesting that these proteins can indeed carry out diverse functional roles. Also, 10 labellar-expressing Obp mutants were developed, and behavioral evidence was obtained that these OBPs may be involved in bitter sensing. The resources constructed in this study should be useful for future Drosophila OBP gene family research. |
| Mukherjee, A., Fallacaro, S., Ratchasanmuang, P., Zinski, J., Boka, A., Shankta, K., Mir, M. (2024). A fine kinetic balance of interactions directs transcription factor hubs to genes. bioRxiv, PubMed ID: 38659757
Summary: Eukaryotic gene regulation relies on the binding of sequence-specific transcription factors (TFs). TFs bind chromatin transiently yet occupy their target sites by forming high-local concentration microenvironments (hubs and condensates) that increase the frequency of binding events. Despite their ubiquity, such microenvironments have been difficult to study in endogenous contexts due to technical limitations. This study overcame these limitations and investigate how hubs drive TF occupancy at their targets. Using a DNA binding perturbation to a hub-forming TF, Zelda, in Drosophila embryos, hub properties, including the stability and frequencies of associations to targets, were found to be key determinants of TF occupancy. These data suggest that the targeting of these hubs was found to be driven not just by specific DNA motif recognition, but also by a fine-tuned kinetic balance of interactions between TFs and their co-binding partners. | Sun, Z., Inagaki, S., Miyoshi, K., Saito, K., Hayashi, S. (2024). Osiris gene family defines the cuticle nanopatterns of Drosophila. Genetics, 227(2) PubMed ID: 38652268
Summary: Nanostructures of pores and protrusions in the insect cuticle modify molecular permeability and surface wetting and help insects sense various environmental cues. However, the cellular mechanisms that modify cuticle nanostructures are poorly understood. Here, we elucidate how insect-specific Osiris family genes are expressed in various cuticle-secreting cells in the Drosophila head during the early stages of cuticle secretion and cover nearly the entire surface of the head epidermis. Furthermore, this study demonstrates how each sense organ cell with various cuticular nanostructures expressed a unique combination of Osiris genes. Osiris gene mutations cause various cuticle defects in the corneal nipples and pores of the chemosensory sensilla. Thus, this study emphasizes on the importance of Osiris genes for elucidating cuticle nanopatterning in insects. |
Monday, February 10th - Larval and Adult Physiology and Metabolism |
| Jia, Q., Yang, L., Wen, J., Liu, S., Wen, D., Luo, W., Wang, W., Palli, S. R., Sheng, L. (2024). Cyp6g2 is the major P450 epoxidase responsible for juvenile hormone biosynthesis in Drosophila melanogaster. BMC Biol, 22(1):111 PubMed ID: 38741075
Summary: Juvenile hormones (JH) play crucial role in regulating development and reproduction in insects. The most common form of JH is JH III, derived from MF through epoxidation by CYP15 enzymes. However, in the higher dipterans, such as the fruitfly, Drosophila melanogaster, a bis-epoxide form of JHB3, accounted most of the JH detected. Moreover, these higher dipterans have lost the CYP15 gene from their genomes. As a result, the identity of the P450 epoxidase in the JH biosynthesis pathway in higher dipterans remains unknown. This study, showed that Cyp6g2 serves as the major JH epoxidase responsible for the biosynthesis of JHB3 and JH III in D. melanogaster. The Cyp6g2 is predominantly expressed in the corpus allatum (CA), concurring with the expression pattern of jhamt, another well-studied gene that is crucial in the last steps of JH biosynthesis. Mutation in Cyp6g2 leads to severe disruptions in larval-pupal metamorphosis and exhibits reproductive deficiencies, exceeding those seen in jhamt mutants. Notably, Cyp6g2-/-::jhamt2 double mutants all died at the pupal stage but could be rescued through the topical application of JH analogs. JH titer analyses revealed that both Cyp6g2-/- mutant and jhamt2 mutant lacking JHB3 and JH III, while overexpression of Cyp6g2 or jhamt caused a significant increase in JHB3 and JH III titer. These findings collectively established that Cyp6g2 as the major JH epoxidase in the higher dipterans and laid the groundwork for the further understanding of JH biosynthesis. Moreover, these findings pave the way for developing specific Cyp6g2 inhibitors as insect growth regulators or insecticides. | Liu, M., He, L. (2024). Dietary cysteine and methionine promote peroxisome elevation and fat loss by induction of CG33474 expression in Drosophila adipose tissue. Cell Mol Life Sci, 81(1):190 PubMed ID: 38649521
Summary: The high-protein diet (HPD) has emerged as a potent dietary approach to curb obesity. Peroxisomes, highly malleable organelles, adapt to nutritional changes to maintain homeostasis by remodeling its structure, composition, and quantity. However, the impact of HPD on peroxisomes and the underlying mechanism remains elusive. Using Drosophila melanogaster as a model system, HPD was fount to specifically increase peroxisome levels within the adipose tissues. This HPD-induced peroxisome elevation is attributed to cysteine and methionine by triggering the expression of http://CG33474, a fly homolog of mammalian PEX11G. Both the overexpression of Drosophila CG33474 and human PEX11G result in increased peroxisome size. In addition, cysteine and methionine diets both reduce lipid contents, a process that depends on the presence of CG33474. Furthermore, CG33474 stimulates the breakdown of neutral lipids in a cell-autonomous manner. Moreover, the expression of CG33474 triggered by cysteine and methionine requires TOR signaling. Finally, CG33474 was found to promote inter-organelle contacts between peroxisomes and lipid droplets (LDs), which might be a potential mechanism for CG33474-induced fat loss. In summary, these findings demonstrate that CG33474/PEX11G may serve as an essential molecular bridge linking HPD to peroxisome dynamics and lipid metabolism. |
| Jin, L., Tian, X., Ji, X., Xiao, G. (2024). The expression of Catsup in the hindgut is essential for zinc homeostasis in Drosophila melanogaster. Insect Mol Biol, PubMed ID: 38664880
Summary: Zinc excretion is crucial for zinc homeostasis. However, the mechanism of zinc excretion has not been well characterized. Zinc homeostasis in Drosophila seems well conserved to mammals. This study screened all members of the zinc transporters ZnT (SLC30) and Zip (SLC39) for their potential roles in Drosophila hindgut, an insect organ that belongs to the excretory system. The results indicated that Catecholamines up (Catsup, CG10449), a ZIP member localized to the Golgi, is responsible for zinc homeostasis in the hindgut of Drosophila hindgut-specific knockdown of Catsup leads to a developmental arrest in the larval stage, which could be rescued well by human ZIP7. Further study suggested that Catsup RNAi in the hindgut reduced zinc levels in the excretory system (containing the Malpighian tubule and hindgut) but exhibited systemic zinc overload. Besides, more calculi were observed in the Malpighian tubules of Catsup RNAi flies. The developmental arrest and calculi in the Malpighian tubules of hindgut-specific Catsup RNAi flies could be rescued by dietary zinc restriction but hypersensitivity to zinc. These results will help us understand the fundamental process of zinc excretion in higher eukaryotes. | Zerva, M. C., Triantafylloudis, C., Paspaliaris, V., Skoulakis, E. M. C., Papanikolopoulou, K. (2024). Choline Metabolites Reverse Differentially the Habituation Deficit and Elevated Memory of Tau Null Drosophila. Cells, 13(9) PubMed ID: 38727282
Summary: Impaired neuronal plasticity and cognitive decline are cardinal features of Alzheimer's disease and related Tauopathies. Aberrantly modified Tau protein and neurotransmitter imbalance, predominantly involving acetylcholine, have been linked to these symptoms. In Drosophila, this study showed that dTau loss specifically enhances associative long-term olfactory memory, impairs foot shock habituation, and deregulates proteins involved in the regulation of neurotransmitter levels, particularly acetylcholine. Interestingly, upon choline treatment, the habituation and memory performance of mutants are restored to that of control flies. Based on these surprising results, a well-established genetic model was used to understand how habituation deficits and memory performance correlate with different aspects of choline physiology as an essential component of the neurotransmitter acetylcholine, the lipid phosphatidylcholine, and the osmoregulator betaine. The results revealed that the two observed phenotypes are reversed by different choline metabolites, implying that they are governed by different underlying mechanisms. This work can contribute to a broader knowledge about the physiologic function of Tau, which may be translated into understanding the mechanisms of Tauopathies. |
| Berger, M., Fraatz, M., Auweiler, K., Dorn, K., El Khadrawe, T., Scholz, H. (2024). Octopamine integrates the status of internal energy supply into the formation of food-related memories. Elife, 12 PubMed ID: 38655926
Summary: The brain regulates food intake in response to internal energy demands and food availability. However, can internal energy storage influence the type of memory that is formed? This study shows that the duration of starvation determines whether Drosophila melanogaster forms appetitive short-term or longer-lasting intermediate memories. The internal glycogen storage in the muscles and adipose tissue influences how intensely sucrose-associated information is stored. Insulin-like signaling in octopaminergic reward neurons integrates internal energy storage into memory formation. Octopamine, in turn, suppresses the formation of long-term memory. Octopamine is not required for short-term memory because octopamine-deficient mutants can form appetitive short-term memory for sucrose and to other nutrients depending on the internal energy status. The reduced positive reinforcing effect of sucrose at high internal glycogen levels, combined with the increased stability of food-related memories due to prolonged periods of starvation, could lead to increased food intake. | Gao, J., Zhang, S., Deng, P., Wu, Z., Lemaitre, B., Zhai, Z., Guo, Z. (2024). Dietary L-Glu sensing by enteroendocrine cells adjusts food intake via modulating gut PYY/NPF secretion. Nat Commun, 15(1):3514 PubMed ID: 38664401
Summary: Amino acid availability is monitored by animals to adapt to their nutritional environment. Beyond gustatory receptors and systemic amino acid sensors, enteroendocrine cells (EECs) are believed to directly percept dietary amino acids and secrete regulatory peptides. However, the cellular machinery underlying amino acid-sensing by EECs and how EEC-derived hormones modulate feeding behavior remain elusive. Ty developing tools to specifically manipulate EECs, this study found that Drosophila neuropeptide F (NPF) from mated female EECs inhibits feeding, similar to human PYY. Mechanistically, dietary L-Glutamate acts through the metabotropic glutamate receptor mGluR to decelerate calcium oscillations in EECs, thereby causing reduced NPF secretion via dense-core vesicles. Furthermore, two dopaminergic enteric neurons expressing http://NPFR perceive EEC-derived NPF and relay an anorexigenic signal to the brain. Thus, these findings provide mechanistic insights into how EECs assess food quality and identify a conserved mode of action that explains how gut NPF/PYY modulates food intake. |
Friday, February 7th - RNA, Transposoons, and RNAi |
| Nikonova, E., DeCata, J., Canela, M., Barz, C., Esser, A., Bouterwek, J., Roy, A., Gensler, H., Hess, M., Straub, T., Forne, I., Spletter, M. L. (2024). Bruno 1/CELF regulates splicing and cytoskeleton dynamics to ensure correct sarcomere assembly in Drosophila flight muscles. PLoS Biol, 22(4):e3002575 PubMed ID: 38683844
Summary: Muscles undergo developmental transitions in gene expression and alternative splicing that are necessary to refine sarcomere structure and contractility. CUG-BP and ETR-3-like (CELF) family RNA-binding proteins are important regulators of RNA processing during myogenesis that are misregulated in diseases such as Myotonic Dystrophy Type I (DM1). This study reports a conserved function for Bruno 1 (Bru1, Arrest), a CELF1/2 family homolog in Drosophila, during early muscle myogenesis. Loss of Bru1 in flight muscles results in disorganization of the actin cytoskeleton leading to aberrant myofiber compaction and defects in pre-myofibril formation. Temporally restricted rescue and RNAi knockdown demonstrate that early cytoskeletal defects interfere with subsequent steps in sarcomere growth and maturation. Early defects are distinct from a later requirement for bru1 to regulate sarcomere assembly dynamics during myofiber maturation. An imbalance in growth in sarcomere length and width was identifed during later stages of development as the mechanism driving abnormal radial growth, myofibril fusion, and the formation of hollow myofibrils in bru1 mutant muscle. Molecularly, we characterize a genome-wide transition from immature to mature sarcomere gene isoform expression was characterize in flight muscle development that is blocked in bru1 mutants. It was further demonstrated that temporally restricted Bru1 rescue can partially alleviate hypercontraction in late pupal and adult stages, but it cannot restore myofiber function or correct structural deficits. These results reveal the conserved nature of CELF function in regulating cytoskeletal dynamics in muscle development and demonstrate that defective RNA processing due to misexpression of CELF proteins causes wide-reaching structural defects and progressive malfunction of affected muscles that cannot be rescued by late-stage gene replacement. | Srivastav, S. P., Feschotte, C., Clark, A. G. (2024). Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary. Genome research, 34(5):711-724 PubMed ID: 38749655
Summary: The piRNA pathway is a highly conserved mechanism to repress transposable element (TE) activity in the animal germline via a specialized class of small RNAs called piwi-interacting RNAs (piRNAs). piRNAs are produced from discrete genomic regions called piRNA clusters (piCs). Although the molecular processes by which piCs function are relatively well understood in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC origin and evolution, a population genomic approach was used to compare piC activity and sequence composition across eight geographically distant strains of D. melanogaster with high-quality long-read genome assemblies. Annotations of ovary piCs and genome-wide TE content was performed in each strain. This analysis uncovers extensive variation in piC activity across strains and signatures of rapid birth and death of piCs. Most TEs inferred to be recently active show an enrichment of insertions into old and large piCs, consistent with the previously proposed "trap" model of piC evolution. In contrast, a small subset of active LTR families is enriched for the formation of new piCs, suggesting that these TEs have higher proclivity to form piCs. Thus, these findings uncover processes leading to the origin of piCs. It is proposed that piC evolution begins with the emergence of piRNAs from individual insertions of a few select TE families prone to seed new piCs that subsequently expand by accretion of insertions from most other TE families during evolution to form larger "trap" clusters. This study shows that TEs themselves are the major force driving the rapid evolution of piCs. |
| Teng, Z., Yang, L., Zhang, Q., Chen, Y., Wang, X., Zheng, Y., Tian, A., Tian, D., Lin, Z., Deng, W. M., Liu, H. (2024). Topoisomerase I is an Evolutionarily Conserved Key Regulator for Satellite DNA Transcription. bioRxiv, PubMed ID: 38746280
Summary: Repetitive satellite DNAs, divergent in nucleic-acid sequence and size across eukaryotes, provide a physical site for centromere assembly to orchestrate chromosome segregation during the cell cycle. These non-coding DNAs are transcribed by RNA polymerase (RNAP) II and the transcription has been shown to play a role in chromosome segregation, but a little is known about the regulation of centromeric transcription, especially in higher organisms with tandemly-repeated-DNA-sequence centromeres. Using RNA interference knockdown, chemical inhibition and AID/IAA degradation, this study showed that Topoisomerase I (TopI), not TopII, promotes the transcription of α-satellite DNAs, the main type of satellite on centromeres in human cells. Mechanistically, TopI localizes to centromeres, binds RNAP II and facilitates RNAP II elongation on centromeres. Interestingly, in response to DNA double-stranded breaks (DSBs) induced by chemotherapy drugs or CRSPR/Cas9, α-satellite transcription is dramatically stimulated in a DNA damage checkpoint-independent but TopI-dependent manner. These DSB-induced α-satellite RNAs were predominantly derived from the α-satellite high-order repeats of human centromeres and forms into strong speckles in the nucleus. Remarkably, TopI-dependent satellite transcription also exists in mouse 3T3 and Drosophila S2 cells and in Drosophila larval imaginal wing discs and tumor tissues. Altogether, these findings herein reveal an evolutionally conserved mechanism with TopI as a key player for the regulation of satellite transcription at both cellular and animal levels. | Biswas, S., Gurdziel, K., Meller, V. H. (2024). siRNA that participates in Drosophila dosage compensation is produced by many 1.688X and 359 bp repeats. Genetics, 227(3) PubMed ID: 38718207
Summary: Organisms with differentiated sex chromosomes must accommodate unequal gene dosage in males and females. Male fruit flies increase X-linked gene expression to compensate for hemizygosity of their single X chromosome. Full compensation requires localization of the Male-Specific Lethal (MSL) complex to active genes on the male X, where it modulates chromatin to elevate expression. The mechanisms that identify X chromatin are poorly understood. The euchromatic X is enriched for AT-rich, ∼359 bp satellites termed the 1.688X rrepeats. Autosomal insertions of 1.688X DNA enable MSL recruitment to nearby genes. Ectopic expression of dsRNA from one of these repeats produces siRNA and partially restores X-localization of MSLs in males with defective X recognition. Surprisingly, expression of double-stranded RNA from three other 1.688X repeats failed to rescue males. This study reconstructed dsRNA-expressing transgenes with sequence from two of these repeats and identified phasing of repeat DNA, rather than sequence or orientation, as the factor that determines rescue of males with defective X recognition. Small RNA sequencing revealed that siRNA was produced in flies with a transgene that rescues, but not in those carrying a transgene with the same repeat but different phasing. Pericentromeric X heterochromatin promotes X recognition through a maternal effect, potentially mediated by small RNA from closely related heterochromatic repeats. This suggests that the sources of siRNAs promoting X recognition are highly redundant. It is proposed that enrichment of satellite repeats on Drosophilid X chromosomes facilitates the rapid evolution of differentiated sex chromosomes by marking the X for compensation. |
| Aute, R., Waghela, N., Deshmukh, M. V. (2024). Key arginine residues in R2D2 dsRBD1 and dsRBD2 lead the siRNA recognition in Drosophila melanogaster RNAi pathway. Biophysical chemistry, 310:107247 PubMed ID: 38663122
Summary: In Drosophila melanogaster, Dcr-2:R2D2 heterodimer binds to the 21 nucleotide siRNA duplex to form the R2D2/Dcr-2 Initiator (RDI) complex, which is critical for the initiation of siRNA-induced silencing complex (RISC) assembly. During RDI complex formation, R2D2, a protein that contains three dsRNA binding domains (dsRBD), senses two aspects of the siRNA: thermodynamically more stable end (asymmetry sensing) and the 5'-phosphate (5'-P) recognition. Despite several detailed studies to date, the molecular determinants arising from R2D2 for performing these two tasks remain elusive. In this study, structural, biophysical, and biochemical characterization of R2D2 dsRBDs was performed. The solution NMR-derived structure of R2D2 dsRBD1 yielded a canonical α1-β1-β2-β3-α2 fold, wherein two arginine salt bridges provide additional stability to the R2D2 dsRBD1. Furthermore, R2D2 dsRBD1 interacts with thermodynamically asymmetric siRNA duplex independent of its 5'-phosphorylation state, whereas R2D2 dsRBD2 prefers to interact with 5'-P siRNA duplex. The mutation of key arginine residues, R53 and R101, in concatenated dsRBDs of R2D2 results in a significant loss of siRNA duplex recognition. This study deciphers the active roles of R2D2 dsRBDs by showing that dsRBD1 initiates siRNA recognition, whereas dsRBD2 senses 5'-phosphate as an authentic mark on functional siRNA. | Komori, H., Rastogi, G., Bugay, J. P., Luo, H., Lin, S., Angers, S., Smibert, C. A., Lipshitz, H. D., Lee, C. Y. (2024). Post-transcriptional regulatory pre-complex assembly drives timely cell-state transitions during differentiation. bioRxiv, PubMed ID: 38746105
Summary: Complexes that control mRNA stability and translation promote timely cell-state transitions during differentiation by ensuring appropriate expression patterns of key developmental regulators. The Drosophila RNA-binding protein Brain tumor (Brat) promotes degradation of target transcripts during the maternal-to-zygotic transition in syncytial embryos and in uncommitted intermediate neural progenitors (immature INPs). Ubiquitin-specific protease 5 (Usp5) was identified as a Brat interactor essential for the degradation of Brat target mRNAs in both cell types. Usp5 promotes Brat-dedadenylase pre-complex assembly in mitotic neural stem cells (neuroblasts) by bridging Brat and the scaffolding components of deadenylase complexes lacking their catalytic subunits. The adaptor protein Miranda binds the RNA-binding domain of Brat, limiting its ability to bind target mRNAs in mitotic neuroblasts. Cortical displacement of Miranda activates Brat-mediated mRNA decay in immature INPs. It is proposed that the assembly of an enzymatically inactive and RNA-binding-deficient pre-complex poises mRNA degradation machineries for rapid activation driving timely developmental transitions. |
Wednesday, February 5th - Evolution |
| Wei, K. H., Chatla, K., Bachtrog, D. (2024). Single-cell RNA-seq of Drosophila miranda testis reveals the evolution and trajectory of germline sex chromosome regulation. PLoS Biol, 22(4):e3002605 PubMed ID: 38687805
Summary: Although sex chromosomes have evolved from autosomes, they often have unusual regulatory regimes that are sex- and cell-type-specific such as dosage compensation (DC) and meiotic sex chromosome inactivation (MSCI). The molecular mechanisms and evolutionary forces driving these unique transcriptional programs are critical for genome evolution but have been, in the case of MSCI in Drosophila, subject to continuous debate. This study took advantage of the younger sex chromosomes in D. miranda (XR and the neo-X) to infer how former autosomes acquire sex-chromosome-specific regulatory programs using single-cell and bulk RNA sequencing and ribosome profiling, in a comparative evolutionary context. Contrary to mammals and worms, the X down-regulation through germline progression was found to be most consistent with the shutdown of DC instead of MSCI, resulting in half gene dosage at the end of meiosis for all 3 X's. Moreover, lowly expressed germline and meiotic genes on the neo-X are ancestrally lowly expressed, instead of acquired suppression after sex linkage. For the young neo-X, DC is incomplete across all tissue and cell types and this dosage imbalance is rescued by contributions from Y-linked gametologs which produce transcripts that are translated to compensate both gene and protein dosage. An excess was found of previously autosomal testis genes becoming Y-specific, showing that the neo-Y and its masculinization likely resolve sexual antagonism. Multicopy neo-sex genes are predominantly expressed during meiotic stages of spermatogenesis, consistent with their amplification being driven to interfere with mendelian segregation. Altogether, this study reveals germline regulation of evolving sex chromosomes and elucidates the consequences these unique regulatory mechanisms have on the evolution of sex chromosome architecture. | Chen, S., Fan, H., Ran, C., Hong, Y., Feng, H., Yue, Z., Zhang, H., Pontarotti, P., Xu, A., Huang, S. (2024). The IL-17 pathway intertwines with neurotrophin and TLR/IL-1R pathways since its domain shuffling origin. Proc Natl Acad Sci U S A, 121(19):e2400903121 PubMed ID: 38683992
Summary: The IL-17 pathway displays remarkably diverse functional modes between different subphyla, classes, and even orders, yet its driving factors remains elusive. This study demonstrates that the IL-17 pathway originated through domain shuffling between a Toll-like receptor (TLR)/IL-1R pathway and a neurotrophin-RTK (receptor-tyrosine-kinase) pathway (a Trunk-Torso pathway). Unlike other new pathways that evolve independently, the IL-17 pathway remains intertwined with its donor pathways throughout later evolution. This intertwining not only influenced the gains and losses of domains and components in the pathway but also drove the diversification of the pathway's functional modes among animal lineages. For instance, this study revealed that the crustacean female sex hormone, a neurotrophin inducing sex differentiation, could interact with IL-17Rs and thus be classified as true IL-17s. Additionally, the insect prothoracicotropic hormone, a neurotrophin initiating ecdysis in Drosophila by binding to Torso, could bind to IL-17Rs in other insects. Furthermore, IL-17R and TLR/IL-1R pathways maintain crosstalk in amphioxus and zebrafish. Moreover, the loss of the Death domain in the pathway adaptor connection to IκB kinase and stress-activated protein kinase (CIKSs) dramatically reduced their abilities to activate nuclear factor-kappaB (NF-κB) and activator protein 1 (AP-1) in amphioxus and zebrafish. Reinstating this Death domain not only enhanced NF-κB/AP-1 activation but also strengthened anti-bacterial immunity in zebrafish larvae. This could explain why the mammalian IL-17 pathway, whose CIKS also lacks Death, is considered a weak signaling activator, relying on synergies with other pathways. These findings provide insights into the functional diversity of the IL-17 pathway and unveil evolutionary principles that could govern the pathway and be used to redesign and manipulate it. |
| Lee, U., Li, C., Langer, C. B., Svetec, N., Zhao, L. (2024). Comparative Single Cell Analysis of Transcriptional Bursting Reveals the Role of Genome Organization on de novo Transcript Origination. bioRxiv, PubMed ID: 38746255
Summary: Spermatogenesis is a key developmental process underlying the origination of newly evolved genes. However, rapid cell type-specific transcriptomic divergence of the Drosophila germline has posed a significant technical barrier for comparative single-cell RNA-sequencing (scRNA-Seq) studies. By quantifying a surprisingly strong correlation between species-and cell type-specific divergence in three closely related Drosophila species, a simple statistical procedure was applied to identify a core set of 198 genes that are highly predictive of cell type identity while remaining robust to species-specific differences that span over 25-30 million years of evolution. Cell type classifications based on the 198-gene set was used to show how transcriptional divergence in cell type increases throughout spermatogenic developmental time, contrasting with traditional hourglass models of whole-organism development. With these cross-species cell type classifications, the influence was then investigated of genome organization on the molecular evolution of spermatogenesis vis-a-vis transcriptional bursting. This study first demonstrated how mechanistic control of pre-meiotic transcription is achieved by altering transcriptional burst size while post-meiotic control is exerted via altered bursting frequency. It is then reported how global differences in autosomal vs. X chromosomal transcription likely arise in a developmental stage preceding full testis organogenesis by showing evolutionarily conserved decreases in X-linked transcription bursting kinetics in all examined somatic and germline cell types. Finally, evidence is provided supporting the cultivator model of de novo gene origination by demonstrating how the appearance of newly evolved testis-specific transcripts potentially provides short-range regulation of the transcriptional bursting properties of neighboring genes during key stages of spermatogenesis. | Singleton, M. D., Eisen, M. B. (2024). Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation. PLoS Comput Biol, 20(4):e1012028 PubMed ID: 38662765
Summary: Intrinsically disordered regions (IDRs) are segments of proteins without stable three-dimensional structures. As this flexibility allows them to interact with diverse binding partners, IDRs play key roles in cell signaling and gene expression. Despite the prevalence and importance of IDRs in eukaryotic proteomes and various biological processes, associating them with specific molecular functions remains a significant challenge due to their high rates of sequence evolution. However, by comparing the observed values of various IDR-associated properties against those generated under a simulated model of evolution, a recent study found most IDRs across the entire yeast proteome contain conserved features. Furthermore, it showed clusters of IDRs with common "evolutionary signatures," i.e. patterns of conserved features, were associated with specific biological functions. To determine if similar patterns of conservation are found in the IDRs of other systems, a series of phylogenetic models were applied to over 7,500 orthologous IDRs identified in the Drosophila genome to dissect the forces driving their evolution. By comparing models of constrained and unconstrained continuous trait evolution using the Brownian motion and Ornstein-Uhlenbeck models, respectively, this study identified signals of widespread constraint, indicating conservation of distributed features is mechanism of IDR evolution common to multiple biological systems. In contrast to the previous study in yeast, however, limited evidence of IDR clusters with specific biological functions was observed, which suggests a more complex relationship between evolutionary constraints and function in the IDRs of multicellular organisms. |
| Audet, T., Krol, J., Pelletier, K., Stewart, A. D., Dworkin, I. (2024). Sexually discordant selection is associated with trait-specific morphological changes and a complex genomic response. Evolution, 78(8):1426-1440 PubMed ID: 38720526
Summary: Sexes often have differing fitness optima, potentially generating intra-locus sexual conflict, as each sex bears a genetic "load" of alleles beneficial to the other sex. One strategy to evaluate conflict in the genome is to artificially select populations discordantly against established sexual dimorphism (SD), reintroducing attenuated conflict. This study investigate a long-term artificial selection experiment reversing sexual size dimorphism in Drosophila melanogaster during ~350 generations of sexually discordant selection. Morphological and genomic changes were observed to identify loci under selection between the sexes in discordantly and concordantly size-selected treatments. Despite substantial changes to overall size, concordant selection maintained ancestral SD. However, discordant selection altered size dimorphism in a trait-specific manner. Multiple possible soft selective sweeps were observed in the genome, with size-related genes showing signs of selection. Patterns of genomic differentiation between the sexes within lineages identified potential sites maintained by sexual conflict. One discordant selected lineage shows a pattern of elevated genomic differentiation between males and females on chromosome 3L, consistent with the maintenance of sexual conflict. These results suggest visible signs of conflict and differentially segregating alleles between the sexes due to discordant selection. | Li, C., Yang, Z., Xu, X., Meng, L., Liu, S., Yang, D. (2024). Conserved and specific gene expression patterns in the embryonic development of tardigrades. Evol Dev, 26(3):e12476 PubMed ID: 38654704
Summary: Tardigrades, commonly known as water bears, are enigmatic organisms characterized by their remarkable resilience to extreme environments despite their simple and compact body structure. To date, there is still much to understand about their evolutionary and developmental features contributing to their special body plan and abilities. This research provides preliminary insights on the conserved and specific gene expression patterns during embryonic development of water bears, focusing on the species Hypsibius exemplaris. The developmental dynamic expression analysis of the genes with various evolutionary age grades indicated that the mid-conserved stage of H. exemplaris corresponds to the period of ganglia and midgut development, with the late embryonic stage showing a transition from non-conserved to conserved state. Additionally, a comparison with Drosophila melanogaster highlighted the absence of certain pathway nodes in development-related pathways, such as Maml and Hairless, which are respectively the transcriptional co-activator and co-repressor of NOTCH regulated genes. Weighted Gene Co-expression Network Analysis (WGCNA) was employed to investigate the expression patterns of tardigrade-specific genes during embryo development. These findings indicated that the module containing the highest proportion of tardigrade-specific genes (TSGs) exhibits high expression levels before the mid-conserved stage, potentially playing a role in glutathione and lipid metabolism. These functions may be associated to the ecdysone synthesis and storage cell formation, which is unique to tardigrades. |
Tuesday, February 4th - Adult Neural Structure, Function and Development |
| Baumann, N. S., Sears, J. C., Broadie, K. (2024). Experience-dependent MAPK/ERK signaling in glia regulates critical period remodeling of synaptic glomeruli. Cell Signal, 120:111224 PubMed ID: 38740233
Summary: Early-life critical periods allow initial sensory experience to remodel brain circuitry so that synaptic connectivity can be optimized to environmental input. In the Drosophila juvenile brain, olfactory sensory neuron (OSN) synaptic glomeruli are pruned by glial phagocytosis in dose-dependent response to early odor experience during a well-defined critical period. Extracellular signal-regulated kinase (ERK) separation of phases-based activity reporter of kinase (SPARK) biosensors reveal experience-dependent signaling in glia during this critical period. Glial ERK-SPARK signaling is depressed by removal of Draper receptors orchestrating glial phagocytosis. Cell-targeted genetic knockdown of glial ERK signaling reduces olfactory experience-dependent glial pruning of the OSN synaptic glomeruli in a dose-dependent mechanism. Noonan Syndrome is caused by gain-of-function mutations in protein tyrosine phosphatase non-receptor type 11 (PTPN11) inhibiting ERK signaling, and a glial-targeted patient-derived mutation increases experience-dependent glial ERK signaling and impairs experience-dependent glial pruning of the OSN synaptic glomeruli. It is concluded that critical period experience drives glial ERK signaling that is required for dose-dependent pruning of brain synaptic glomeruli, and that altered glial ERK signaling impairs this critical period mechanism in a Noonan Syndrome disease model. | Brown, M. P., Verma, S., Palmer, I., Guerrero Zuniga, A., Mehta, A., Rosensweig, C., Keles, M. F., Wu, M. N. (2024). A subclass of evening cells promotes the switch from arousal to sleep at dusk. Curr Biol, 34(10):2186-2199.e2183 PubMed ID: 38723636
Summary: Animals exhibit rhythmic patterns of behavior that are shaped by an internal circadian clock and the external environment. Although light intensity varies across the day, there are particularly robust differences at twilight (dawn/dusk). These periods are also associated with major changes in behavioral states, such as the transition from arousal to sleep. However, the neural mechanisms by which time and environmental conditions promote these behavioral transitions are poorly defined. This study showed that the E1 subclass of Drosophila evening clock neurons promotes the transition from arousal to sleep at dusk. It was first demonstrated that the cell-autonomous clocks of E2 neurons primarily drive and adjust the phase of evening anticipation, the canonical behavior associated with "evening" clock neurons. This study next showed that conditionally silencing E1 neurons causes a significant delay in sleep onset after dusk. However, rather than simply promoting sleep, activating E1 neurons produces time- and light-dependent effects on behavior. Activation of E1 neurons has no effect early in the day but then triggers arousal before dusk and induces sleep after dusk. Strikingly, these activation-induced phenotypes depend on the presence of light during the day. Despite their influence on behavior around dusk, in vivo voltage imaging of E1 neurons reveals that their spiking rate and pattern do not significantly change throughout the day. Moreover, E1-specific clock ablation has no effect on arousal or sleep. Thus, it is suggested that, rather than specifying "evening" time, E1 neurons act, in concert with other rhythmic neurons, to promote behavioral transitions at dusk. |
| Donovan, E. J., Agrawal, A., Liberman, N., Kalai, J. I., Adler, A. J., Lamper, A. M., Wang, H. Q., Chua, N. J., Koslover, E. F., Barnhart, E. L. (2024). Dendrite architecture determines mitochondrial distribution patterns in vivo. Cell Rep, 43(5):114190 PubMed ID: 38717903
Summary: Neuronal morphology influences synaptic connectivity and neuronal signal processing. However, it remains unclear how neuronal shape affects steady-state distributions of organelles like mitochondria. This work investigated the link between mitochondrial transport and dendrite branching patterns by combining mathematical modeling with in vivo measurements of dendrite architecture, mitochondrial motility, and mitochondrial localization patterns in Drosophila HS (horizontal system) neurons. In this model, different forms of morphological and transport scaling rules-which set the relative thicknesses of parent and daughter branches at each junction in the dendritic arbor and link mitochondrial motility to branch thickness-predict dramatically different global mitochondrial localization patterns. HS dendrites were shown to obey the specific subset of scaling rules that, in this model, lead to realistic mitochondrial distributions. Moreover, neuronal activity does not affect mitochondrial transport or localization, indicating that steady-state mitochondrial distributions are hard-wired by the architecture of the neuron. | Puri, P., Wu, S. T., Su, C. Y., Aljadeff, J. (2024). Peripheral preprocessing in Drosophila facilitates odor classification. Proc Natl Acad Sci. 121(21):e2316799121.PubMed ID: 38753511
Summary: The mammalian brain implements sophisticated sensory processing algorithms along multilayered ("deep") neural networks. Strategies that insects use to meet similar computational demands, while relying on smaller nervous systems with shallow architectures, remain elusive. Using Drosophila as a model, this study uncovered the algorithmic role of odor preprocessing by a shallow network of compartmentalized olfactory receptor neurons. Each compartment operates as a ratiometric unit for specific odor-mixtures. This computation arises from a simple mechanism: electrical coupling between two differently sized neurons. Downstream synaptic connectivity is shaped to optimally leverage amplification of a hedonic value signal in the periphery. Furthermore, peripheral preprocessing is shown to markedly improve novel odor classification in a higher brain center. Together, thia work highlights a far-reaching functional role of the sensory periphery for downstream processing. By elucidating the implementation of powerful computations by a shallow network, we provide insights into general principles of efficient sensory processing algorithms. |
| Christenson, M. P., Sanz Diez, A., Heath, S. L., Saavedra-Weisenhaus, M., Adachi, A., Nern, A., Abbott, L. F., Behnia, R. (2024). Hue selectivity from recurrent circuitry in Drosophila. Nat Neurosci, 27(6):1137-1147 PubMed ID: 38755272
Summary: In the perception of color, wavelengths of light reflected off objects are transformed into the derived quantities of brightness, saturation and hue. Neurons responding selectively to hue have been reported in primate cortex, but it is unknown how their narrow tuning in color space is produced by upstream circuit mechanisms. This study reports the discovery of neurons in the Drosophila optic lobe with hue-selective properties, which enables circuit-level analysis of color processing. From analysis of an electron microscopy volume of a whole Drosophila brain, this study constructed a connectomics-constrained circuit model that accounts for this hue selectivity. The model predicts that recurrent connections in the circuit are critical for generating hue selectivity. Experiments using genetic manipulations to perturb recurrence in adult flies confirm this prediction. These findings reveal a circuit basis for hue selectivity in color vision. | Bustillo, M. E., Douthit, J., Astigarraga, S., Treisman, J. E. (2024). Two distinct mechanisms of Plexin A function in Drosophila optic lobe lamination and morphogenesis. Development, 151(10) PubMed ID: 38738602
Summary: Visual circuit development is characterized by subdivision of neuropils into layers that house distinct sets of synaptic connections. In the Drosophila medulla, this layered organization depends on the axon guidance regulator Plexin A. In Plexin A null mutants, synaptic layers of the medulla neuropil and arborizations of individual neurons are wider and less distinct than in controls. Analysis of semaphorin function indicates that Semaphorin 1a, acting in a subset of medulla neurons, is the primary partner for Plexin A in medulla lamination. Removal of the cytoplasmic domain of endogenous Plexin A has little effect on the formation of medulla layers; however, both null and cytoplasmic domain deletion mutations of Plexin A result in an altered overall shape of the medulla neuropil. These data suggest that Plexin A acts as a receptor to mediate morphogenesis of the medulla neuropil, and as a ligand for Semaphorin 1a to subdivide it into layers. Its two independent functions illustrate how a few guidance molecules can organize complex brain structures by each playing multiple roles. |
Monday, February 3rd - Disease Models |
| Tao, X., Liu, J., Diaz-Perez, Z., Foley, J. R., Nwafor, A., Stewart, T. M., Casero, R. A., Jr., Zhai, R. G. (2024). Reduction of spermine synthase enhances autophagy to suppress Tau accumulation. Cell Death Dis, 15(5):333 PubMed ID: 38740758
Summary: Precise polyamine metabolism regulation is vital for cells and organisms. Mutations in spermine synthase (SMS) cause Snyder-Robinson intellectual disability syndrome (SRS), characterized by significant spermidine accumulation and autophagy blockage in the nervous system. Emerging evidence connects polyamine metabolism with other autophagy-related diseases, such as Tauopathy, however, the functional intersection between polyamine metabolism and autophagy in the context of these diseases remains unclear. This study altered SMS expression level to investigate the regulation of autophagy by modulated polyamine metabolism in Tauopathy in Drosophila and human cellular models. Interestingly, while complete loss of Drosophila Spermine synthase (dSms) impairs lysosomal function and blocks autophagic flux recapitulating SRS disease phenotype, partial loss of dSms enhanced autophagic flux, reduced Tau protein accumulation, and led to extended lifespan and improved climbing performance in Tauopathy flies. Measurement of polyamine levels detected a mild elevation of spermidine in flies with partial loss of dSms. Similarly, in human neuronal or glial cells, partial loss of SMS by siRNA-mediated knockdown upregulated autophagic flux and reduced Tau protein accumulation. Importantly, proteomics analysis of postmortem brain tissue from Alzheimer's disease (AD) patients showed a significant albeit modest elevation of SMS level. Taken together, this study uncovers a functional correlation between polyamine metabolism and autophagy in AD: SMS reduction upregulates autophagy, suppresses Tau accumulation, and ameliorates neurodegeneration and cell death. These findings provide a new potential therapeutic target for AD. | Gao, Y. H., Wen, D. T., Du, Z. R., Wang, J. F., Wang, S. J. (2024). Muscle Psn gene combined with exercise contribute to healthy aging of skeletal muscle and lifespan by adaptively regulating Sirt1/PGC-1α and arm pathway. PLoS One, 19(5):e0300787 PubMed ID: 38753634
Summary: The Presenilin (Psn) gene is closely related to aging, but it is still unclear the role of Psn genes in skeletal muscle. In this study, the Psn-UAS/Mhc-GAL4 system in Drosophila was used to regulate muscle Psn overexpression(MPO) and muscle Psn knockdown(MPK). Drosophila were subjected to endurance exercise from 4 weeks to 5 weeks old. The results showed that MPO and exercise significantly increased climbing speed, climbing endurance, lifespan, muscle SOD activity, Psn expression, Sirt1 expression, PGC-1α expression, and armadillo (arm) expression in aged Drosophila, and they significantly decreased muscle malondialdehyde levels. Interestingly, when the Psn gene is knockdown by 0.78 times, the PGC-1α expression and arm expression were also down-regulated, but the exercise capacity and lifespan were increased. Furthermore, exercise combined with MPO further improved the exercise capacity and lifespan. MPK combined with exercise further improves the exercise capacity and lifespan. Thus, current results confirmed that the muscle Psn gene was a vital gene that contributed to the healthy aging of skeletal muscle since whether it was overexpressed or knocked down, the aging progress of skeletal muscle structure and function was slowed down by regulating the activity homeostasis of Sirt1/PGC-1α pathway and Psn/arm pathway. Exercise enhanced the function of the Psn gene to delay skeletal muscle aging by up regulating the activity of the Sirt1/PGC-1α pathway and Psn/arm pathway. |
| Droppelmann, C. A., Campos-Melo, D., Noches, V., McLellan, C., Szabla, R., Lyons, T. A., Amzil, H., Withers, B., Kaplanis, B., Sonkar, K. S., Simon, A., Buratti, E., Junop, M., Kramer, J. M., Strong, M. J. (2024). Mitigation of TDP-43 toxic phenotype by an RGNEF fragment in amyotrophic lateral sclerosis models. Brain : a journal of neurology, 147(6):2053-2068 PubMed ID: 38739752
Summary: Aggregation of the RNA-binding protein TAR DNA binding protein (TDP-43) is a hallmark of TDP-proteinopathies including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). As TDP-43 aggregation and dysregulation are causative of neuronal death, there is a special interest in targeting this protein as a therapeutic approach. Previous work found that TDP-43 extensively co-aggregated with the dual function protein GEF (guanine exchange factor) and RNA-binding protein rho guanine nucleotide exchange factor (RGNEF) in ALS patients. This study shows that an N-terminal fragment of RGNEF (NF242) interacts directly with the RNA recognition motifs of TDP-43 competing with RNA and that the IPT/TIG domain of NF242 is essential for this interaction. Genetic expression of NF242 in a fruit fly ALS model overexpressing TDP-43 suppressed the neuropathological phenotype increasing lifespan, abolishing motor defects and preventing neurodegeneration. Intracerebroventricular injections of AAV9/NF242 in a severe TDP-43 murine model (rNLS8) improved lifespan and motor phenotype, and decreased neuroinflammation markers. These results demonstrate an innovative way to target TDP-43 proteinopathies using a protein fragment with a strong affinity for TDP-43 aggregates and a mechanism that includes competition with RNA sequestration, suggesting a promising therapeutic strategy for TDP-43 proteinopathies such as ALS and FTD. | Jullian, E., Russi, M., Turki, E., Bouvelot, M., Tixier, L., Middendorp, S., Martin, E., Monnier, V. (2024). Glial overexpression of Tspo extends lifespan and protects against frataxin deficiency in Drosophila. Biochimie, 224:71-79 PubMed ID: 38750879
Summary: The translocator protein TSPO is an evolutionary conserved mitochondrial protein overexpressed in various contexts of neurodegeneration. Friedreich Ataxia (FA) is a neurodegenerative disease due to GAA expansions in the FXN gene leading to decreased expression of frataxin, a mitochondrial protein involved in the biosynthesis of iron-sulfur clusters. Previously Tspo was overexpressed in a Drosophila model of this disease generated by CRISPR/Cas9 insertion of approximately 200 GAA in the intron of fh, the fly frataxin gene. This study describes a new Drosophila model of FA with 42 GAA repeats, called fh-GAAs. The smaller expansion size allowed to obtain adults exhibiting hallmarks of the FA disease, including short lifespan, locomotory defects and hypersensitivity to oxidative stress. The reduced lifespan was fully rescued by ubiquitous expression of human FXN, confirming that both frataxins share conserved functions. Tspo was overexpressed in heads and decreased in intestines of these fh-GAAs flies. Then, Tspo was further overexpressed specifically in glial cells and improved survival was observed. Finally, the effects were investigated of Tspo overexpression in healthy flies. Increased longevity was conferred by glial-specific overexpression, with opposite effects in neurons. Overall, this study highlights protective effects of glial TSPO in Drosophila both in a neurodegenerative and a healthy context. |
| Weisz, E. D., Fenton, A. R., Jongens, T. A. (2024). PGC-1α integrates insulin signaling with mitochondrial physiology and behavior in a Drosophila model of Fragile X Syndrome. NPJ metabolic health and disease, 2:2 PubMed ID: 38741938
Summary: Fragile X Syndrome (FXS) is the most prevalent monogenetic form of intellectual disability and autism. Recently, dysregulation of insulin signaling (IS) and aberrations in mitochondrial function have emerged as robust, evolutionarily conserved components of FXS pathophysiology. However, the mechanisms by which altered IS and mitochondrial dysfunction impact behavior in the context of FXS remain elusive. This study shows that normalization of IS improves mitochondrial volume and function in flies that lack expression of dfmr1, the Drosophila homolog of the causal gene of FXS in humans. Further, dysregulation of IS underlies diminished expression of the mitochondrial master regulator PGC-1α/Spargel in dfmr1 mutant flies. These results are behaviorally relevant, as pan-neuronal augmentation of PGC-1α/Spargel improves circadian behavior in >dfmr1 mutants. Notably, this study also showed that modulation of PGC-1α/Spargel expression in wild-type flies phenocopies the >dfmr1 mutant circadian defect. Taken together, these results provide a mechanistic link between mitochondrial function and circadian behavior both in FXS pathogenesis as well as more broadly at the interface between metabolism and behavioral output. | Mou, W., Tang, Y., Huang, Y., Wu, Z., Cui, Y. (2024). Upregulation of neuronal ER-phagy improves organismal fitness and alleviates APP toxicity. Cell Rep, 43(5):114255 PubMed ID: 38761376
Summary: ER-phagy, a selective autophagy targeting the endoplasmic reticulum (ER) for lysosomal degradation through cargo receptors, plays a critical role in ER quality control and is linked to various diseases. However, its physiological and pathological roles remain largely unclear due to a lack of animal model studies. This study establishes Drosophila as an in vivo ER-phagy model. Starvation triggers ER-phagy across multiple fly tissues. Disturbing ER-phagy by either globally upregulating or downregulating ER-phagy receptors, Atl or Rtnl1, harms the fly. Notably, moderate upregulation of ER-phagy in fly brains by overexpressing Atl or Rtnl1 significantly attenuates age-associated neurodegenerations. Furthermore, in a Drosophila model of Alzheimer's disease expressing human amyloid precursor protein (APP), impaired ER-phagy is observed. Enhancing ER-phagy in the APP-expressing fly brain facilitates APP degradation, significantly alleviating disease symptoms. Therefore, these findings suggest that modulating ER-phagy may offer a therapeutic strategy to treat aging and diseases associated with ER protein aggregation. |
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