What's hot today: Current papers in developmental biology and gene function Follow @interactivefly Tweet

Monday, May 16th

Sayal, R., Dresch, J.M., Pushel, I., Taylor, B.R. and Arnosti, D.N. (2016). Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo. Elife 5. PubMed ID: 27152947 Summary: Enhancers constitute one of the major components of regulatory machinery of metazoans. Although several genome-wide studies have focused on finding and locating enhancers in the genomes, the fundamental principles governing their internal architecture and cis-regulatory grammar remain elusive. This study describes an extensive, quantitative perturbation analysis targeting the dorsal-ventral patterning gene regulatory network (GRN) controlled by Drosophila NF-κB homolog Dorsal. To understand transcription factor interactions on enhancers, an ensemble of mathematical models were employed to test effects of cooperativity, repression, and factor potency. Models trained on the dataset correctly predict activity of evolutionarily divergent regulatory regions, providing insights into spatial relationships between repressor and activator binding sites. Importantly, the collective predictions of sets of models are effective at novel enhancer identification and characterization. The study demonstrates how experimental dataset and modeling can be effectively combined to provide quantitative insights into cis-regulatory information on a genome-wide scale.

Jia, D., Bryant, J., Jevitt, A., Calvin, G. and Deng, W. M. (2016). The ecdysone and Notch pathways synergistically regulate Cut at the dorsal-ventral boundary in Drosophila wing discs. J Genet Genomics [Epub ahead of print]. PubMed ID: 27117286 Summary: Metazoan development requires coordination of signaling pathways to regulate patterns of gene expression. In Drosophila, the wing imaginal disc provides an excellent model for the study of how signaling pathways interact to regulate pattern formation. The determination of the dorsal-ventral (DV) boundary of the wing disc depends on the Notch pathway, which is activated along the DV boundary and induces the expression of the homeobox transcription factor, Cut. This study shows that Broad (Br), a zinc-finger transcription factor, is also involved in regulating Cut expression in the DV boundary region. However, Br expression is not regulated by Notch signaling in wing discs, ecdysone signaling is the upstream signal that induces Br for Cut upregulation. Also, it was found that the ecdysone-Br cascade upregulates cut-lacZ expression, a reporter containing a 2.7 kb cut enhancer region, implying that ecdysone signaling, similar to Notch, regulates cut at the transcriptional level. Collectively, these findings reveal that the Notch and ecdysone signaling pathways synergistically regulate Cut expression for proper DV boundary formation in the wing disc. Additionally, br was shown to promote Delta, a Notch ligand, near the DV boundary to suppress aberrant high Notch activity, indicating further interaction between the two pathways for DV patterning of the wing disc.

Samee, M. A., Lim, B., Samper, N., Lu, H., Rushlow, C. A., Jimenez, G., Shvartsman, S. Y. and Sinha, S. (2015). A systematic ensemble approach to thermodynamic modeling of gene expression from sequence data. Cell Syst 1: 396-407. PubMed ID: 27136354 Summary: To understand the relationship between an enhancer DNA sequence and quantitative gene expression, thermodynamics-driven mathematical models of transcription are often employed. These 'sequence-to-expression' models can describe an incomplete or even incorrect set of regulatory relationships if the parameter space is not searched systematically. This study focused on an enhancer of the Drosophila gene ind and demonstrate how a systematic search of parameter space can reveal a more comprehensive picture of a gene's regulatory mechanisms, resolve outstanding ambiguities, and suggest testable hypotheses. An approach is described that generates an ensemble of ind models; all of these models are technically acceptable solutions to the sequence-to-expression problem in light of wild-type data, and some represent mechanistically distinct hypotheses about the regulation of ind. This ensemble can be restricted to biologically plausible models using requirements gleaned from in vivo perturbation experiments. Biologically plausible models make unique predictions about how specific ind enhancer sequences affect ind expression; these predictions were validated in vivo through site mutagenesis in transgenic Drosophila embryos.

Spirov, A. V., Myasnikova, E. M. and Holloway, D. M. (2016). Sequential construction of a model for modular gene expression control, applied to spatial patterning of the Drosophila gene hunchback. J Bioinform Comput Biol 14: 1641005. PubMed ID: 27122317 Summary: Gene network simulations are increasingly used to quantify mutual gene regulation in biological tissues. These are generally based on linear interactions between single-entity regulatory and target genes. Biological genes, by contrast, commonly have multiple, partially independent, cis-regulatory modules (CRMs) for regulator binding, and can produce variant transcription and translation products. This study presents a modeling framework to address some of the gene regulatory dynamics implied by this biological complexity. Spatial patterning of the hunchback (hb) gene in Drosophila development involves control by three CRMs producing two distinct mRNA transcripts. This example was used to develop a differential equations model for transcription which takes into account the cis-regulatory architecture of the gene. Potential regulatory interactions are screened by a genetic algorithms (GAs) approach and compared to biological expression data.

Sunday, May 15th

Hussain, A., Ucpunar, H. K., Zhang, M., Loschek, L. F. and Grunwald Kadow, I. C. (2016). Neuropeptides modulate female chemosensory processing upon mating in Drosophila. PLoS Biol 14: e1002455. PubMed ID: 27145127 Summary: A female's reproductive state influences her perception of odors and tastes along with her changed behavioral state and physiological needs. The mechanism that modulates chemosensory processing, however, remains largely elusive. Using Drosophila, this study has identified a behavioral, neuronal, and genetic mechanism that adapts the senses of smell and taste, the major modalities for food quality perception, to the physiological needs of a gravid female. Pungent smelling polyamines, such as putrescine and spermidine, are essential for cell proliferation, reproduction, and embryonic development in all animals. A polyamine-rich diet increases reproductive success in many species, including flies. Using a combination of behavioral analysis and in vivo physiology, this study shows that polyamine attraction is modulated in gravid females through a G-protein coupled receptor, the sex peptide receptor (SPR), and its neuropeptide ligands, MIPs (myoinhibitory peptides), which act directly in the polyamine-detecting olfactory and taste neurons. This modulation is triggered by an increase of SPR expression in chemosensory neurons, which is sufficient to convert virgin to mated female olfactory choice behavior. Together, these data show that neuropeptide-mediated modulation of peripheral chemosensory neurons increases a gravid female's preference for important nutrients, thereby ensuring optimal conditions for her growing progeny.

Hussain, A., Zhang, M., Ucpunar, H. K., Svensson, T., Quillery, E., Gompel, N., Ignell, R. and Grunwald Kadow, I. C. (2016). Ionotropic chemosensory receptors mediate the taste and smell of polyamines. PLoS Biol 14: e1002454. PubMed ID: 27145030 Summary: The ability to find and consume nutrient-rich diets for successful reproduction and survival is fundamental to animal life. Among the nutrients important for all animals are polyamines, a class of pungent smelling compounds required in numerous cellular and organismic processes. Polyamine deficiency or excess has detrimental effects on health, cognitive function, reproduction, and lifespan. This study shows that a diet high in polyamine is beneficial and increases reproductive success of flies and unravels the sensory mechanisms that attract Drosophila to polyamine-rich food and egg-laying substrates. Using a combination of behavioral genetics and in vivo calcium imaging, Drosophila was shown to use multisensory detection to find and evaluate polyamines present in overripe and fermenting fruit, their favored feeding and egg-laying substrate. In the olfactory system, two coexpressed ionotropic receptors (IRs), IR76b and IR41a, mediate the long-range attraction to the odor. In the gustatory system, multimodal taste sensation by IR76b receptor and GR66a bitter receptor neurons is used to evaluate quality and valence of the polyamine providing a mechanism for the fly's high attraction to polyamine-rich and sweet decaying fruit. Given their universal and highly conserved biological roles, it is proposed that the ability to evaluate food for polyamine content may impact health and reproductive success also of other animals including humans.

Ko, K. I., Root, C. M., Lindsay, S. A., Zaninovich, O. A., Shepherd, A. K., Wasserman, S. A., Kim, S. M. and Wang, J. W. (2015). Starvation promotes concerted modulation of appetitive olfactory behavior via parallel neuromodulatory circuits. Elife 4. PubMed ID: 26208339 Summary: The internal state of an organism influences its perception of attractive or aversive stimuli and thus promotes adaptive behaviors that increase its likelihood of survival. The mechanisms underlying these perceptual shifts are critical to understanding of how neural circuits support animal cognition and behavior. Starved flies exhibit enhanced sensitivity to attractive odors and reduced sensitivity to aversive odors. This study shows that a functional remodeling of the olfactory map is mediated by two parallel neuromodulatory systems that act in opposing directions on olfactory attraction and aversion at the level of the first synapse. Short neuropeptide F sensitizes an antennal lobe glomerulus wired for attraction, while tachykinin (DTK) suppresses activity of a glomerulus wired for aversion. Thus this study shows parallel neuromodulatory systems functionally reconfigure early olfactory processing to optimize detection of nutrients at the risk of ignoring potentially toxic food resources.

Navawongse, R., Choudhury, D., Raczkowska, M., Stewart, J. C., Lim, T., Rahman, M., Toh, A. G., Wang, Z. and Claridge-Chang, A. (2016). Drosophila learn efficient paths to a food source. Neurobiol Learn Mem 131: 176-181. PubMed ID: 27063671 Summary: Elucidating the genetic, and neuronal bases for learned behavior is a central problem in neuroscience. Methods to study adaptive food-seeking behavior in Drosophila have lagged decades behind rodent feeding analysis, largely due to the challenges presented by their small scale. There is currently no method to dynamically control flies' access to food. In rodents, protocols that use dynamic food delivery are a central element of experimental paradigms that date back to the influential work of Skinner. This method is still commonly used in the analysis of learning, memory, addiction, feeding, and many other subjects in experimental psychology. The difficulty of microscale food delivery means this is not a technique used in fly behavior. In this paper describe a microfluidic chip integrated with machine vision and automation to dynamically control defined liquid food presentations and sensory stimuli. Strikingly, repeated presentations of food at a fixed location produced improvements in path efficiency during food approach. This shows that improved path choice is a learned behavior. Active control of food availability using this microfluidic system is a valuable addition to the methods currently available for the analysis of learned feeding behavior in flies.

Saturday, May 14th

Tsai, H. Z., Lin, R. K. and Hsieh, T. S. (2016). Drosophila mitochondrial topoisomerase III alpha affects the aging process via maintenance of mitochondrial function and genome integrity. J Biomed Sci 23: 38. PubMed ID: 27067525 Summary: Mitochondria play important roles in providing metabolic energy and key metabolites for synthesis of cellular building blocks. Mitochondria have additional functions in other cellular processes, including programmed cell death and aging. A previous study revealed Drosophila mitochondrial topoisomerase III α (Top3α) contributes to the maintenance of the mitochondrial genome and male germ-line stem cells. However, the involvement of mitochondrial Top3α in the mitochondrion-mediated aging process remains unclear. In this study, the M1L flies, in which Top3α protein lacks the mitochondrial import sequence and is thus present in cell nuclei but not in mitochondria, were used as a model system to examine the role of mitochondrial Top3α in the aging of fruit flies. M1L flies were shown to exhibit mitochondrial defects which affect the aging process. First, it was observed that M1L flies have a shorter life span, which was correlated with a significant reduction in the mitochondrial DNA copy number, the mitochondrial membrane potential, and ATP content compared with those of both wild-type and transgene-rescued flies of the same age. Second, a mobility assay and electron microscopic analysis was performed to demonstrate that the locomotion defect and mitophagy of M1L flies were enhanced with age, as compared with the controls. Finally, it was shown that the correlation between the mtDNA deletion level and aging in M1L flies resembles what was reported in mammalian systems. The results demonstrate that mitochondrial Top3α ablation results in mitochondrial genome instability and its dysfunction, thereby accelerating the aging process.

Xu, W., et al. (2016). Amyloid precursor protein-mediated endocytic pathway disruption induces axonal dysfunction and neurodegeneration. J Clin Invest [Epub ahead of print]. PubMed ID: 27064279 Summary: The endosome/lysosome pathway is disrupted early in the course of both Alzheimer's disease (AD) and Down syndrome (DS); however, it is not clear how dysfunction in this pathway influences the development of these diseases. This study explored the cellular and molecular mechanisms by which endosomal dysfunction contributes to the pathogenesis of AD and DS. It was determined that full-length amyloid precursor protein (APP; see Drosophila Appl) and its β-C-terminal fragment (β-CTF) act though increased activation of Rab5 to cause enlargement of early endosomes and to disrupt retrograde axonal trafficking of nerve growth factor (NGF) signals. The functional impacts of APP and its various products were investigated in PC12 cells, cultured rat basal forebrain cholinergic neurons (BFCNs), and BFCNs from a mouse model of DS. The full-length wild-type APP (APPWT) and β-CTF both induced endosomal enlargement and disrupted NGF signaling and axonal trafficking. β-CTF alone induced atrophy of BFCNs that was rescued by the dominant-negative Rab5 mutant, Rab5S34N. Moreover, expression of a dominant-negative Rab5 construct markedly reduced APP-induced axonal blockage in Drosophila. Therefore, increased APP and/or β-CTF impact the endocytic pathway to disrupt NGF trafficking and signaling, resulting in trophic deficits in BFCNs. These data strongly support the emerging concept that dysregulation of Rab5 activity contributes importantly to early pathogenesis of AD and DS.

Achal, M., et al. (2016). A restrictive cardiomyopathy mutation in an invariant proline at the myosin head/rod junction enhances head flexibility and function, yielding muscle defects in Drosophila. J Mol Biol [Epub ahead of print]. PubMed ID: 27107639 Summary: An 'invariant proline' separates the myosin S1 head from its S2 tail and is proposed to be critical for orienting S1 during its interaction with actin, a process that leads to muscle contraction. Mutation of the invariant proline to leucine (P838L) caused dominant restrictive cardiomyopathy in a pediatric patient. This study used Drosophila to model this mutation. P838L mutant myosin isolated from indirect flight muscles of transgenic Drosophila showed elevated ATPase and actin sliding velocity in vitro. Further, the mutant heads exhibited increased rotational flexibility and there was an increase in the average angle between the two heads. Indirect flight muscle myofibril assembly was minimally affected in mutant homozygotes and isolated fibers displayed normal mechanical properties. However, myofibrils degraded during aging, correlating with reduced flight abilities. In contrast, hearts from homozygotes and heterozygotes showed normal morphology, myofibrillar arrays and contractile parameters. Overall, the studies suggest that increased rotational flexibility of myosin S1 enhances myosin ATPase and actin sliding. Further, instability of P838L myofibrils leads to decreased function during aging of Drosophila skeletal muscle, but not cardiac muscle, despite the strong evolutionary conservation of the P838 residue.

Barekat, A., et al. (2016). Using Drosophila as an integrated model to study mild repetitive traumatic brain injury. Sci Rep 6: 25252. PubMed ID: 27143646 Summary: Traumatic brain injury (TBI) is a major cause of morbidity and mortality worldwide. In addition, there has been a growing appreciation that even repetitive, milder forms of TBI (mTBI) can have long-term deleterious consequences to neural tissues. Hampering understanding of genetic and environmental factors that influence the cellular and molecular responses to injury has been the limited availability of effective genetic model systems that could be used to identify the key genes and pathways that modulate both the acute and long-term responses to TBI. This study reports the development of a severe and mild-repetitive TBI model using Drosophila. Using this system, key features that are typically found in mammalian TBI models were also identified in flies, including the activation of inflammatory and autophagy responses, increased Tau phosphorylation and neuronal defects that impair sleep-related behaviors. This novel injury paradigm demonstrates the utility of Drosophila as an effective tool to validate genetic and environmental factors that influence the whole animal response to trauma and to identify prospective therapies needed for the treatment of TBI.

Friday, May 13th

Tseng, C. Y., Kao, S. H. and Hsu, H. J. (2016). Snail controls proliferation of Drosophila ovarian epithelial follicle stem cells, independently of E-cadherin. Dev Biol [Epub ahead of print]. PubMed ID: 27141871 Summary: Epithelial-mesenchymal transition (EMT), which is primarily mediated by Snail via the suppression of E-cadherin, is able to generate cells with stem cell properties. However, the role of Snail in epithelial stem cells remains unclear. This study reports that Snail directly controls proliferation of follicle stem cells (FSCs) in Drosophila females. Disruption of Snail expression in FSCs compromises their proliferation, but not their maintenance. Conversely, FSCs with excessive Snail expression display increased proliferation and lifespan, which is accompanied by a moderate decrease in the expression of E-cadherin (required for adhesion of FSCs to their niche) at the junction between their adjacent cells, indicating a conserved role of Snail in E-cadherin inhibition, which promote epithelial cell proliferation. Interestingly, a decrease in E-cadherin in snail-knock down FSCs does not restore the decreased proliferation of snail-knock down FSCs, suggesting that adhesion strength of FSCs to their niche is dispensable for Snail-mediated FSC division. These results demonstrate that Snail controls epithelial stem cell division independently of its known role in the EMT, which contributes to induction of cancer stem cells.

Upadhyay, M., Martino Cortez, Y., Wong-Deyrup, S., Tavares, L., Schowalter, S., Flora, P., Hill, C., Nasrallah, M. A., Chittur, S. and Rangan, P. (2016). Transposon dysregulation modulates dWnt4 signaling to control germline stem cell differentiation in Drosophila. PLoS Genet 12: e1005918. PubMed ID: 27019121 Summary: Germline stem cell (GSC) self-renewal and differentiation are required for the sustained production of gametes. GSC differentiation in Drosophila oogenesis requires expression of the histone methyltransferase dSETDB1/Eggless by the somatic niche, however its function in this process is unknown. This study shows that dSETDB1 is required for the expression of a Wnt ligand, Wnt4, in the somatic niche. Wnt4 signaling acts on the somatic niche cells to facilitate their encapsulation of the GSC daughter, which serves as a differentiation cue. dSETDB1 is known to repress transposable elements (TEs) to maintain genome integrity. Unexpectedly, this study found that independent upregulation of TEs also downregulated Wnt4, leading to GSC differentiation defects. This suggests that Wnt4 expression is sensitive to the presence of TEs. Together these results reveal a chromatin-transposon-Wnt signaling axis that regulates stem cell fate.

Elgart, M., Stern, S., Salton, O., Gnainsky, Y., Heifetz, Y. and Soen, Y. (2016). Impact of gut microbiota on the fly's germ line. Nat Commun 7: 11280. PubMed ID: 27080728 Summary: Unlike vertically transmitted endosymbionts, which have broad effects on their host's germ line, the extracellular gut microbiota is transmitted horizontally and is not known to influence the germ line. This study provides evidence supporting the influence of these gut bacteria on the germ line of Drosophila melanogaster. Removal of the gut bacteria represses oogenesis, expedites maternal-to-zygotic-transition in the offspring and unmasks hidden phenotypic variation in mutants. It was further shown that the main impact on oogenesis is linked to the lack of gut Acetobacter species, and the Drosophila Aldehyde dehydrogenase (Aldh) gene was identified as an apparent mediator of repressed oogenesis in Acetobacter-depleted flies. The finding of interactions between the gut microbiota and the germ line has implications for reproduction, developmental robustness and adaptation.

Sanghavi, P., Liu, G., Veeranan-Karmegam, R., Navarro, C. and Gonsalvez, G. B. (2016). Multiple roles for Egalitarian in polarization of the Drosophila egg chamber. Genetics [Epub ahead of print]. PubMed ID: 27017624 Summary: RNA-binding protein Egalitarian (Egl) is required for specification and maintenance of oocyte fate. Mutants in egl either completely fail to specify an oocyte, or if specified, the oocyte eventually reverts back to nurse cell fate. Due to this very early role for Egl in egg chamber maturation, it is unclear whether later stages of egg chamber development also require Egl function. In this study, Egl was depleted at specific stages of egg chamber development. In early stage egg chambers, Egl was shown to have an additional role in organization of oocyte microtubules. In the absence of Egl function, oocyte microtubules completely fail to reorganize. As such, the localization of microtubule motors and their cargo is disrupted. In addition, Egl also appears to function in regulating the translation of critical polarity determining mRNAs. Finally, in mid stage egg chambers, Egl does not appear to be required for microtubule organization, but rather for the correct spatial localization of oskar, bicoid and gurken mRNAs.

Thursday, May 12th

Chen, D.Y., Lipari, K.R., Dehghan, Y., Streichan, S.J. and Bilder, D. (2016). Symmetry breaking in an edgeless epithelium by Fat2-regulated microtubule polarity. Cell Rep [Epub ahead of print]. PubMed ID: 27134170 Summary: Planar cell polarity (PCP) information is a critical determinant of organ morphogenesis. While PCP in bounded epithelial sheets is increasingly well understood, how PCP is organized in tubular and acinar tissues is not known. Drosophila egg chambers (follicles) are an acinus-like "edgeless epithelium" and exhibit a continuous, circumferential PCP that does not depend on pathways active in bounded epithelia; this follicle PCP directs formation of an ellipsoid rather than a spherical egg. This study uses an imaging algorithm to "unroll" the entire 3D tissue surface and comprehensively analyze PCP onset. This approach traces chiral symmetry breaking to plus-end polarity of microtubules in the germarium, well before follicles form and rotate. PCP germarial microtubules provide chiral information that predicts the direction of whole-tissue rotation as soon as independent follicles form. Concordant microtubule polarity, but not microtubule alignment, requires the atypical cadherin Fat2, which acts at an early stage to translate plus-end bias into coordinated actin-mediated collective cell migration. Because microtubules are not required for PCP or migration after follicle rotation initiates, while dynamic actin and extracellular matrix are, polarized microtubules lie at the beginning of a handoff mechanism that passes early chiral PCP of the cytoskeleton to a supracellular planar polarized extracellular matrix and elongates the organ.

Han, Y., Shi, Q. and Jiang, J. (2015). Multisite interaction with Sufu regulates Ci/Gli activity through distinct mechanisms in Hh signal transduction. Proc Natl Acad Sci U S A 112: 6383-6388. PubMed ID: 25941387 Summary: The tumor suppressor protein Suppressor of fused (Sufu) plays a conserved role in the Hedgehog (Hh) signaling pathway by inhibiting Cubitus interruptus (Ci)/Glioma-associated oncogene homolog (Gli) transcription factors, but the molecular mechanism by which Sufu inhibits Ci/Gli activity remains poorly understood. This study shows that Sufu can bind Ci/Gli through a C-terminal Sufu-interacting site (SIC) in addition to a previously identified N-terminal site (SIN), and that both SIC and SIN are required for optimal inhibition of Ci/Gli by Sufu. Sufu can sequester Ci/Gli in the cytoplasm through binding to SIN while inhibiting Ci/Gli activity in the nucleus depending on SIC. It was also found that binding of Sufu to SIC and the middle region of Ci can impede recruitment of the transcriptional coactivator CBP by masking its binding site in the C-terminal region of Ci. Indeed, moving the CBP-binding site to an 'exposed' location can render Ci resistant to Sufu-mediated inhibition in the nucleus. Hence, this study identifies a previously unidentified and conserved Sufu-binding motif in the C-terminal region of Ci/Gli and provides mechanistic insight into how Sufu inhibits Ci/Gli activity in the nucleus.

Le, T.P., Vuong, L.T., Kim, A.R., Hsu, Y.C. and Choi, K.W. (2016). 14-3-3 proteins regulate Tctp-Rheb interaction for organ growth in Drosophila. Nat Commun 7: 11501. PubMed ID: 27151460 Summary: 14-3-3 family proteins regulate multiple signalling pathways. Understanding biological functions of 14-3-3 proteins has been limited by the functional redundancy of conserved isotypes. This study provides evidence that 14-3-3 proteins regulate two interacting components of Tor signalling in Drosophila, translationally controlled tumour protein (Tctp) and Rheb GTPase. Single knockdown of 14-3-3ɛ or 14-3-3ζ isoform does not show obvious defects in organ development but causes synergistic genetic interaction with Tctp and Rheb to impair tissue growth. 14-3-3 proteins physically interact with Tctp and Rheb. Knockdown of both 14-3-3 isoforms abolishes the binding between Tctp and Rheb, disrupting organ development. Depletion of 14-3-3s also reduces the level of phosphorylated S6 kinase, phosphorylated Thor/4E-BP and cyclin E (CycE). Growth defects from knockdown of 14-3-3 and Tctp are suppressed by CycE overexpression. This study suggests a novel mechanism of Tor regulation mediated by 14-3-3 interaction with Tctp and Rheb.

Liu, X., Greer, C. and Secombe, J. (2014). KDM5 interacts with Foxo to modulate cellular levels of oxidative stress. PLoS Genet 10: e1004676. PubMed ID: 25329053 Summary: Increased cellular levels of oxidative stress are implicated in a large number of human diseases. This study describes the transcription co-factor KDM5 (also known as Lid) as a new critical regulator of cellular redox state. Moreover, this occurs through a novel KDM5 activity whereby it alters the ability of the transcription factor Foxo to bind to DNA. Microarray analyses of kdm5 mutants revealed a striking enrichment for genes required to regulate cellular levels of oxidative stress. Consistent with this, loss of kdm5 results in increased sensitivity to treatment with oxidizers, elevated levels of oxidized proteins, and increased mutation load. KDM5 activates oxidative stress resistance genes by interacting with Foxo to facilitate its recruitment to KDM5-Foxo co-regulated genes. Significantly, this occurs independently of KDM5's well-characterized demethylase activity. Instead, KDM5 interacts with the lysine deacetylase HDAC4 to promote Foxo deacetylation, which affects Foxo DNA binding.

Wednesday, May 11th

Saberi, M. and Seyed-Allaei, H. (2016). Odorant receptors of Drosophila are sensitive to the molecular volume of odorants. Sci Rep 6: 25103. PubMed ID: 27112241 Summary: Which properties of a molecule define its odor? This is a basic yet unanswered question regarding the olfactory system. The olfactory system of Drosophila has a repertoire of approximately 60 odorant receptors. Molecules bind to odorant receptors with different affinities and activate them with different efficacies, thus providing a combinatorial code that identifies odorants. This study hypothesized that the binding affinity of an odorant-receptor pair is affected by their relative sizes. The maximum affinity can be attained when the molecular volume of an odorant matches the volume of the binding pocket. The affinity drops to zero when the sizes are too different, thus obscuring the effects of other molecular properties. A mathematical formulation of this hypothesis was developed and verified using Drosophila data. The volume and structural flexibility of the binding site of each odorant receptor were also predicted; these features significantly differ between odorant receptors. The differences in the volumes and structural flexibilities of different odorant receptor binding sites may explain the difference in the scents of similar molecules with different sizes.

Vogt, K., Aso, Y., Hige, T., Knapek, S., Ichinose, T., Friedrich, A. B., Turner, G. C., Rubin, G. M. and Tanimoto, H. (2016). Direct neural pathways convey distinct visual information to mushroom bodies. Elife 5. PubMed ID: 27083044. Journal and Pubmed Summary: Previous studies have identified that visual and olfactory associative memories of Drosophila share the mushroom body (MB) circuit. Despite well-characterized odor representations in the Drosophila MB, the MB circuit for visual information is totally unknown. This study shows that a small subset of MB Kenyon cells (KCs) selectively responds to visual but not olfactory stimulation. The dendrites of these atypical KCs form a ventral accessory calyx (vAC), distinct from the main calyx that receives olfactory input. Two types of visual projection neurons (VPNs) directly connecting the optic lobes and the vAC were identified. Strikingly, these VPNs are differentially required for visual memories of color and brightness. The segregation of visual and olfactory domains in the MB allows independent processing of distinct sensory memories and may be a conserved form of sensory representations among insects.

Gai, Y., Liu, Z., Cervantes-Sandoval, I. and Davis, R.L. (2016). DrosophilaSLC22A transporter is a memory suppressor gene that influences cholinergic neurotransmission to the mushroom bodies. Neuron 90: 581-595. PubMed ID: 27146270 Summary: The mechanisms that constrain memory formation are of special interest because they provide insights into the brain's memory management systems and potential avenues for correcting cognitive disorders. RNAi knockdown in the Drosophila mushroom body neurons (MBn) of a newly discovered memory suppressor gene, Solute Carrier DmSLC22A, a member of the organic cation transporter family, enhances olfactory memory expression, while overexpression inhibits it. The protein localizes to the dendrites of the MBn, surrounding the presynaptic terminals of cholinergic afferent fibers from projection neurons (Pn). Cell-based expression assays show that this plasma membrane protein transports cholinergic compounds with the highest affinity among several in vitro substrates. Feeding flies choline or inhibiting acetylcholinesterase in Pn enhances memory, an effect blocked by overexpression of the transporter in the MBn. The data argue that DmSLC22A is a memory suppressor protein that limits memory formation by helping to terminate cholinergic neurotransmission at the Pn:MBn synapse.

Mabuchi, I., Shimada, N., Sato, S., Ienaga, K., Inami, S. and Sakai, T. (2016). Mushroom body signaling is required for locomotor activity rhythms in Drosophila. Neurosci Res [Epub ahead of print]. PubMed ID: 27106579 Summary: In the fruitfly Drosophila melanogaster, circadian rhythms of locomotor activity under constant darkness are controlled by pacemaker neurons. To understand how behavioral rhythmicity is generated by the nervous system, it is essential to identify the output circuits from the pacemaker neurons. The importance of mushroom bodies (MBs) in generating behavioral rhythmicity remains controversial because contradicting results have been reported as follows: (1) locomotor activity in MB-ablated flies is substantially rhythmic, but (2) activation of restricted neuronal populations including MB neurons induces arrhythmic locomotor activity. This study reports that neurotransmission in MBs is required for behavioral rhythmicity. For adult-specific disruption of neurotransmission in MBs, the GAL80/GAL4/UAS ternary gene expression system was used in combination with the temperature-sensitive dynamin mutation shibirets1. Blocking of neurotransmission in GAL4-positive neurons including MB neurons induced arrhythmic locomotor activity, whereas this arrhythmicity was rescued by the MB-specific expression of GAL80. These results indicate that MB signaling plays a key role in locomotor activity rhythms in Drosophila.

Tuesday, May 10

Chen, H., Zheng, X., Xiao, D. and Zheng, Y. (2016). Age-associated de-repression of retrotransposons in the Drosophila fat body, its potential cause and consequence. Aging Cell [Epub ahead of print]. PubMed ID: 27072046 Summary: Eukaryotic genomes contain transposable elements (TE) that can move into new locations upon activation. Since uncontrolled transposition of TEs, including the retrotransposons and DNA transposons, can lead to DNA breaks and genomic instability, multiple mechanisms, including heterochromatin-mediated repression, have evolved to repress TE activation. Studies in model organisms have shown that TEs become activated upon aging as a result of age-associated deregulation of heterochromatin. Considering that different organisms or cell types may undergo distinct heterochromatin changes upon aging, it is important to identify pathways that lead to TE activation in specific tissues and cell types. Through deep sequencing of isolated RNAs, this study report an increased expression of many retrotransposons in the old Drosophila fat body, an organ equivalent to the mammalian liver and adipose tissue. This de-repression correlates with an increased number of DNA damage foci and decreased level of Drosophila lamin-B in the old fat body cells. Depletion of the Drosophila lamin-B in the young or larval fat body results in a reduction of heterochromatin and a corresponding increase in retrotransposon expression and DNA damage. Further manipulations of lamin-B and retrotransposon expression suggest a role of the nuclear lamina in maintaining the genome integrity of the Drosophila fat body by repressing retrotransposons.

Zolotarev, N., Fedotova, A., Kyrchanova, O., Bonchuk, A., Penin, A.A., Lando, A.S., Eliseeva, I.A., Kulakovskiy, I.V., Maksimenko, O. and Georgiev, P. (2016). Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila. Nucleic Acids Res [Epub ahead of print]. PubMed ID: 27137890 Summary: According to recent models, as yet poorly studied architectural proteins appear to be required for local regulation of enhancer-promoter interactions, as well as for global chromosome organization. Transcription factors ZIPIC, Pita and Zw5 belong to the class of chromatin insulator proteins and preferentially bind to promoters near the TSS and extensively colocalize with cohesin and condensin complexes. ZIPIC, Pita and Zw5 are structurally similar in containing the N-terminal zinc finger-associated domain (ZAD) and different numbers of C2H2-type zinc fingers at the C-terminus. This study shows that the ZAD domains of ZIPIC, Pita and Zw5 form homodimers. In Drosophila transgenic lines, these proteins are able to support long-distance interaction between GAL4 activator and the reporter gene promoter. However, no functional interaction between binding sites for different proteins was found, suggesting that such interactions are highly specific. ZIPIC facilitates long-distance stimulation of the reporter gene by GAL4 activator in yeast model system. Many of the genomic binding sites of ZIPIC, Pita and Zw5 are located at the boundaries of topologically associated domains (TADs). Thus, ZAD-containing zinc-finger proteins can be attributed to the class of architectural proteins.

Melnikova, L., Shapovalov, I., Kostyuchenko, M., Georgiev, P. and Golovnin, A. (2016). EAST affects the activity of Su(Hw) insulators by two different mechanisms in Drosophila melanogaster. Chromosoma [Epub ahead of print]. PubMed ID: 27136940 Summary: Recent data suggest that insulators organize chromatin architecture in the nucleus. The best characterized Drosophila insulator, found in the gypsy retrotransposon, contains 12 binding sites for the Su(Hw) protein. Enhancer blocking, along with Su(Hw), requires BTB/POZ domain proteins, Mod(mdg4)-67.2 and CP190. Inactivation of Mod(mdg4)-67.2 leads to a direct repression of the yellow gene promoter by the gypsy insulator. This study shows that such repression is regulated by the level of the EAST protein, which is an essential component of the interchromatin compartment. Deletion of the EAST C-terminal domain suppresses Su(Hw)-mediated repression. Partial inactivation of EAST by mutations in the east gene suppresses the enhancer-blocking activity of the gypsy insulator. The binding of insulator proteins to chromatin is highly sensitive to the level of EAST expression. These results suggest that EAST, one of the main components of the interchromatin compartment, can regulate the activity of chromatin insulators.

Zhang, W., et al. (2016). . The nucleosome remodeling and deacetylase complex NuRD is built from preformed catalytically active sub-modules. J Mol Biol [Epub ahead of print]. PubMed ID: 27117189 Summary: The Nucleosome Remodeling Deacetylase (NuRD) complex is a highly conserved regulator of chromatin structure and transcription. Structural studies have shed light on this and other chromatin modifying machines, but much less is known about how they assemble and whether stable and functional sub-modules exist that retain enzymatic activity. Purification of the endogenous Drosophila NuRD complex shows that it consists of a stable core of subunits, while others, in particular the chromatin remodeller CHD4, associate transiently. To dissect the assembly and activity of NuRD, all possible combinations of different components were systematically produced using the MultiBac system, and their activity and biophysical properties were determined. Single molecule imaging of CHD4 was carried out in live mouse ES cells, in the presence and absence of one of core components (MBD3), to show how the core deacetylase and chromatin-remodeling sub-modules associate in-vivo. These experiments suggest a pathway for the assembly of NuRD via preformed and active sub-modules. These retain enzymatic activity and are present in both the nucleus and the cytosol, an outcome with important implications for understanding NuRD function.

Monday, May 9th

Matsumoto, K., Ayukawa, T., Ishio, A., Sasamura, T., Yamakawa, .T and Matsuno, K. (2016). Dual roles of O-glucose glycans redundant with monosaccharide O-fucose on Notch in Notch trafficking. J Biol Chem [Epub ahead of print]. PubMed ID: 27129198 Summary: The extracellular domain of Notch contains multiple EGF-like repeats. At least five different glycans are found in distinct sites within these EGF-like repeats. The potential functional interactions between these glycans are just beginning to be understood. Monosaccharide O-fucose and O-glucose trisaccharide (O-glucose-xylose-xylose) are added to many of the Notch EGF-like repeats. In Drosophila, Shams adds a xylose specifically to the monosaccharide O-glucose. Loss of the terminal dixylose of O-glucose-linked saccharides has little effect on Notch signaling. Analyses of double mutants of shams and other genes required for glycan modifications reveals that both the monosaccharide O-glucose and the terminal dixylose of O-glucose-linked saccharides function redundantly with the monosaccharide O-fucose in Notch activation and trafficking. The terminal dixylose of O-glucose-linked saccharides and the monosaccharide O-glucose are required in distinct Notch-trafficking processes: Notch transport from the apical plasma membrane to adherens junctions, and Notch export from the endoplasmic reticulum, respectively. Therefore, the monosaccharide O-glucose and terminal dixylose of O-glucose-linked saccharides have distinct activities in Notch trafficking, although a loss of these activities is compensated for by the presence of monosaccharide O-fucose. Given that various glycans attached to a protein motif may have redundant functions, these results suggest that these potential redundancies may lead to a serious underestimation of glycan functions.

Gomez-Lamarca, M. J., Snowdon, L. A., Seib, E., Klein, T. and Bray, S. J. (2015). Rme-8 depletion perturbs Notch recycling and predisposes to pathogenic signaling. J Cell Biol 210: 303-318. PubMed ID: 26169355 Summary: Notch signaling is a major regulator of cell fate, proliferation, and differentiation. Like other signaling pathways, its activity is strongly influenced by intracellular trafficking. Besides contributing to signal activation and down-regulation, differential fluxes between trafficking routes can cause aberrant Notch pathway activation. Investigating the function of the retromer-associated DNAJ protein Rme-8 in vivo, this study demonstrated a critical role in regulating Notch receptor recycling. In the absence of Rme-8, Notch accumulated in enlarged tubulated Rab4-positive endosomes, and as a consequence, signaling was compromised. Strikingly, when the retromer component Vps26 was depleted at the same time, Notch no longer accumulated and instead was ectopically activated. Likewise, depletion of ESCRT-0 components Hrs or Stam in combination with Rme-8 also led to high levels of ectopic Notch activity. Together, these results highlight the importance of Rme-8 in coordinating normal endocytic recycling route and reveal that its absence predisposes toward conditions in which pathological Notch signaling can occur.

Aerne, B. L., Gailite, I., Sims, D. and Tapon, N. (2015). Hippo stabilises its adaptor Salvador by antagonising the HECT ubiquitin ligase Herc4. PLoS One 10: e0131113. PubMed ID: 26125558 Summary: Signalling through the Hippo (Hpo) pathway involves a kinase cascade, which leads to the phosphorylation and inactivation of the pro-growth transcriptional co-activator Yorkie (Yki). Despite the identification of a large number of pathway members and modulators, understanding of the molecular events that lead to activation of Hpo and the downstream kinase Warts (Wts) remain incomplete. Recently, targeted degradation of several Hpo pathway components has been demonstrated as a means of regulating pathway activity. In particular, the stability of scaffold protein Salvador (Sav), which is believed to promote Hpo/Wts association, is crucially dependent on its binding partner Hpo. In a cell-based RNAi screen for ubiquitin regulators involved in Sav stability, this study identified the HECT domain protein Herc4 (HECT and RLD domain containing E3 ligase) as a Sav E3 ligase. Herc4 expression promotes Sav ubiquitylation and degradation, while Herc4 depletion stabilises Sav. Interestingly, Hpo reduces Sav/Herc4 interaction in a kinase-dependent manner. This suggests the existence of a positive feedback loop, where Hpo stabilises its own positive regulator by antagonising Herc4-mediated degradation of Sav.

Cho, B., Pierre-Louis, G., Sagner, A., Eaton, S. and Axelrod, J. D. (2015). Clustering and negative feedback by endocytosis in planar cell polarity signaling is modulated by ubiquitinylation of Prickle. PLoS Genet 11: e1005259. PubMed ID: 25996914 Summary: The core components of the planar cell polarity (PCP) signaling system, including both transmembrane and peripheral membrane associated proteins, form asymmetric complexes that bridge apical intercellular junctions. While these can assemble in either orientation, coordinated cell polarization requires the enrichment of complexes of a given orientation at specific junctions. This might occur by both positive and negative feedback between oppositely oriented complexes, and requires the peripheral membrane associated PCP components. However, the molecular mechanisms underlying feedback are not understood. This study found that the E3 ubiquitin ligase complex Cullin1(Cul1)/SkpA/Supernumerary limbs(Slimb) regulates the stability of one of the peripheral membrane components, Prickle (Pk). Excess Pk disrupts PCP feedback and prevents asymmetry. Pk was found to participate in negative feedback by mediating internalization of PCP complexes containing the transmembrane components Van Gogh (Vang) and Flamingo (Fmi), and that internalization is activated by oppositely oriented complexes within clusters. Pk also participates in positive feedback through an unknown mechanism promoting clustering. these results therefore identify a molecular mechanism underlying generation of asymmetry in PCP signaling.

Sunday, May 8th

Qi, Y., Huang, J., Li, M. Q., Wu, Y. S., Xia, R. Y. and Ye, G. Y. (2016). Serotonin modulates insect hemocyte phagocytosis via two different serotonin receptors. Elife 5 [Epub ahead of print]. PubMed ID: 26974346 Summary: Serotonin (5-HT) modulates both neural and immune responses in vertebrates, but its role in insect immunity remains uncertain. This study reports that hemocytes in the caterpillar, Pieris rapae are able to synthesize 5-HT following activation by lipopolysaccharide. The inhibition of a serotonin-generating enzyme with either pharmacological blockade or RNAi knock-down impaired hemocyte phagocytosis. Biochemical and functional experiments showed that naive hemocytes primarily express 5-HT1B and 5-HT2B receptors. The blockade of 5-HT1B significantly reduced phagocytic ability, however the blockade of 5-HT2B increased hemocyte phagocytosis. The 5-HT1B-null Drosophila melanogaster mutants showed higher mortality than controls when infected with bacteria, due to their decreased phagocytotic ability. Flies expressing 5-HT1B or 5-HT2B RNAi in hemocytes also showed similar sensitivity to infection. Combined, these data demonstrate that 5-HT mediates hemocyte phagocytosis through 5-HT1B and 5-HT2B receptors and serotonergic signaling performs critical modulatory functions in immune systems of animals separated by 500 million years of evolution.

Wong, Z. S., Brownlie, J. C. and Johnson, K. N. (2016). Impact of ERK activation on fly survival and Wolbachia-mediated protection during virus infection. J Gen Virol [Epub ahead of print]. PubMed ID: 26977591 Summary: Elevated levels of reactive oxygen species (ROS) provide protection against virus-induced mortality in Drosophila. In addition to contributing to oxidative stress, ROS are known to activate a number of signaling pathways including the extracellular signal-regulated kinases (ERK) signaling cascade. It was recently shown that ERK signaling is important for resistance against viral replication and invasion in cultured Drosophila cells and the gut epithelium of adult flies. Here, using a Drosophila loss-of-function ERK (rolled) mutant it was demonstrated that ERK is important for fly survival during virus infection. ERK mutant flies subjected to Drosophila C virus (DCV) oral and systemic infection were more susceptible to virus-induced mortality as compared to wild type flies. It was demonstrated experimentally that ERK activation is important for fly survival during oral and systemic virus infection. Given that elevated ROS correlates with Wolbachia-mediated antiviral protection, the involvement of ERK in antiviral protection was also investigated in flies infected by Wolbachia. The results indicate that ERK activation is increased in the presence of Wolbachia but this does not appear to influence Wolbachia-mediated antiviral protection, at least during systemic infection.

Rainey, S. M., et al. (2016). Wolbachia blocks viral genome replication early in infection without a transcriptional response by the endosymbiont or host small RNA pathways. PLoS Pathog 12: e1005536. PubMed ID: 27089431 Summary: The intracellular endosymbiotic bacterium Wolbachia can protect insects against viral infection. To investigate the mechanisms underlying this antiviral protection, this study developed a new model system combining Wolbachia-infected Drosophila melanogaster cell culture with the model mosquito-borne Semliki Forest virus (SFV; Togaviridae, Alphavirus). Wolbachia provides strong antiviral protection rapidly after infection, suggesting that an early stage post-infection is being blocked. Wolbachia does appear to have major effects on events distinct from entry, assembly or exit as it inhibits the replication of an SFV replicon transfected into the cells. Furthermore, it causes a far greater reduction in the expression of proteins from the 3 open reading frame than the 5 non-structural protein open reading frame, indicating that it is blocking the replication of viral RNA. Further to this separation of the replicase proteins and viral RNA in transreplication assays shows that uncoupling of viral RNA and replicase proteins does not overcome Wolbachia's antiviral activity. This further suggests that replicative processes are disrupted, such as translation or replication, by Wolbachia infection. This may occur by Wolbachia mounting an active antiviral response, but the virus did not cause any transcriptional response by the bacterium, suggesting that this is not the case. Host microRNAs (miRNAs) have been implicated in protection, but again it was found that host cell miRNA expression was unaffected by the bacterium and neither do the findings suggest any involvement of the antiviral siRNA pathway. It is concluded that Wolbachia may directly interfere with early events in virus replication such as translation of incoming viral RNA or RNA transcription, and this likely involves an intrinsic (as opposed to an induced) mechanism.

Lamiable, O., Arnold, J., da Silva de Faria, I. J., Proveti Olmo, R., Bergami, F., Meignin, C., Hoffmann, J. A., Marques, J. T. and Imler, J. L. (2016). Analysis of the contribution of hemocytes and autophagy to Drosophila antiviral immunity. J Virol [Epub ahead of print]. PubMed ID: 27009948 Summary: Antiviral immunity in Drosophila involves the broadly active intrinsic mechanism of RNA interference (RNAi) and virus-specific inducible responses. Using a panel of six viruses, this study investigated the role of hemocytes and autophagy in the control of viral infections. Injection of latex beads to saturate phagocytosis, or genetic depletion of hemocytes, resulted in decreased survival and increased viral titers following infection with cricket paralysis virus (CrPV), Flock House Virus (FHV) and vesicular stomatitis virus (VSV), but had no impact on Drosophila C virus (DCV), Sindbis virus (SINV) and invertebrate iridescent virus 6 (IIV6). In the case of CrPV and FHV, apoptosis was induced in infected cells, which were phagocytosed by hemocytes. In contrast, VSV did not trigger any significant apoptosis but the autophagy gene Atg7 was required for full virus resistance, suggesting that hemocytes use autophagy to recognize the virus. However, this recognition does not depend on the Toll-7 receptor. Autophagy had no impact on DCV, CrPV, SINV or IIV6, and was required for replication of the sixth virus, FHV. Even in the case of VSV the increase in titers were modest in Atg7 mutant flies suggesting that autophagy does not play a major role in antiviral immunity in Drosophila Altogether, these results indicate that, while autophagy plays a minor role, phagocytosis contributes to virus-specific immune responses in insects.

Saturday, May 7th

Wang, Q., Taliaferro, J.M., Klibaite, U., Hilgers, V., Shaevitz, J.W. and Rio, D.C. (2016). The PSI-U1 snRNP interaction regulates male mating behavior in Drosophila. Proc Natl Acad Sci U S A [Epub ahead of print]. PubMed ID: 27114556 Summary: Fruitless alternative pre-mRNA splicing (AS) isoforms have been shown to influence male courtship behavior, but the underlying mechanisms are unknown. Using genome-wide approaches and quantitative behavioral assays, this study shows that the P-element somatic inhibitor (PSI) and its interaction with the U1 small nuclear ribonucleoprotein complex (snRNP) control male courtship behavior. PSI mutants lacking the U1 snRNP-interacting domain (PSIΔAB mutant) exhibit extended but futile mating attempts. The PSIΔAB mutant results in significant changes in the AS patterns of ~1,200 genes in the Drosophila brain, many of which have been implicated in the regulation of male courtship behavior. PSI directly regulates the AS of at least one-third of these transcripts, suggesting that PSI-U1 snRNP interactions coordinate the behavioral network underlying courtship behavior. Importantly, one of these direct targets is fruitless, the master regulator of courtship. Thus, PSI imposes a specific mode of regulatory control within the neuronal circuit controlling courtship, even though it is broadly expressed in the fly nervous system. This study reinforces the importance of AS in the control of gene activity in neurons and integrated neuronal circuits, and provides a surprising link between a pleiotropic pre-mRNA splicing pathway and the precise control of successful male mating behavior.

Kopytova, D., Popova, V., Kurshakova, M., Shidlovskii, Y., Nabirochkina, E., Brechalov, A., Georgiev, G. and Georgieva, S. (2016). ORC interacts with THSC/TREX-2 and its subunits promote Nxf1 association with mRNP and mRNA export in Drosophila. Nucleic Acids Res [Epub ahead of print]. PubMed ID: 27016737 Summary: The origin recognition complex (ORC) of eukaryotes associates with the replication origins and initiates the pre-replication complex assembly. In the literature, there are several reports of interaction of ORC with different RNAs. This study demonstrates for the first time a direct interaction of ORC with the THSC/TREX-2 mRNA nuclear export complex. The THSC/TREX-2 was purified from the Drosophila embryonic extract and found to bind with a fraction of the ORC. This interaction occurred via several subunits and was essential for Drosophila viability. Also, ORC was associated with mRNP, which was facilitated by TREX-2. ORC subunits interacted with the Nxf1 receptor mediating the bulk mRNA export. The knockdown of Orc5 led to a drop in the Nxf1 association with mRNP, while Orc3 knockdown increased the level of mRNP-bound Nxf1. The knockdown of Orc5, Orc3 and several other ORC subunits led to an accumulation of mRNA in the nucleus, suggesting that ORC participates in the regulation of the mRNP export.

Macdonald, P. M., Kanke, M. and Kenny, A. (2016). Community effects in regulation of translation. Elife 5 [Epub ahead of print]. PubMed ID: 27104756 Summary: Certain forms of translational regulation, and translation itself, rely on long-range interactions between proteins bound to the different ends of mRNAs. A widespread assumption is that such interactions occur only in cis, between the two ends of a single transcript. However, certain translational regulatory defects of the Drosophila oskar (osk) mRNA can be rescued in trans. It is proposed that inter-transcript interactions, promoted by assembly of the mRNAs in particles, allow regulatory elements to act in trans. This study confirms predictions of that model and shows that disruption of Polypyrimidine tract binding protein (PTB) dependent particle assembly inhibits rescue in trans. Communication between transcripts is not limited to different osk mRNAs, as regulation imposed by cis-acting elements embedded in the osk mRNA spreads to gurken mRNA. It is concluded that community effects exist in translational regulation.

McMahon, A. C., Rahman, R., Jin, H., Shen, J. L., Fieldsend, A., Luo, W. and Rosbash, M. (2016). TRIBE: Hijacking an RNA-editing enzyme to identify cell-specific targets of RNA-binding proteins. Cell 165: 742-753. PubMed ID: 27040499 Summary: RNA transcripts are bound and regulated by RNA-binding proteins (RBPs). Current methods for identifying in vivo targets of an RBP are imperfect and not amenable to examining small numbers of cells. TRIBE (targets of RNA-binding proteins identified by editing) technique that couples an RBP to the catalytic domain of the Drosophila RNA-editing enzyme ADAR and expresses the fusion protein in vivo, was developed to address these issues. RBP targets are marked with novel RNA editing events and identified by sequencing RNA. TRIBE was used to identify the targets of three RBPs (Hrp48, dFMR1, and NonA). TRIBE compares favorably to other methods, including CLIP, and this study has identified RBP targets from as little as 150 specific fly neurons. TRIBE can be performed without an antibody and in small numbers of specific cells.

Friday, May 6th

Yamaki, T., Yasuda, G. K. and Wakimoto, B. T. (2016). The Deadbeat paternal effect of uncapped sperm telomeres on cell cycle progression and chromosome behavior in Drosophila melanogaster. Genetics [Epub ahead of print]. PubMed ID: 27029731 Summary: Telomere-capping complexes (TCCs) protect the ends of linear chromosomes from illegitimate repair and end-to-end fusions and are required for genome stability. The identity and assembly of TCC components have been extensively studied, but whether TCCs require active maintenance in non-dividing cells remains an open question. This study shows that Drosophila melanogaster requires Deadbeat (Ddbt), a sperm nuclear basic protein (SNBP) that is recruited to the telomere by the TCC and is required for TCC maintenance during genome-wide chromatin remodeling that transforms spermatids to mature sperm. Ddbt-deficient males produce sperm lacking TCCs. Their offspring delay the initiation of anaphase as early as cycle 1 but progress through the first two cycles. Persistence of uncapped paternal chromosomes induces arrest at or around cycle 3. This early arrest can be rescued by selective elimination of paternal chromosomes and production of gynogenetic haploid or haploid mosaics. Progression past cycle 3 can also occur if embryos have reduced levels of the maternally provided checkpoint kinase Chk2. The findings provide insights into how telomere integrity affects the regulation of the earliest embryonic cell cycles. They also suggest that other SNBPs, including those in humans, may have analogous roles and manifest as paternal effects on embryo quality.

Tao, L., Fasulo, B., Warecki, B. and Sullivan, W. (2016). Tum/RacGAP functions as a switch activating the Pav/kinesin-6 motor. Nat Commun 7: 11182. PubMed ID: 27091402 Summary: Centralspindlin is essential for central spindle and cleavage furrow formation. Drosophila centralspindlin consists of a kinesin-6 motor (Pav/kinesin-6) and a GTPase-activating protein (Tum/RacGAP). Centralspindlin localization to the central spindle is mediated by Pav/kinesin-6. While Tum/RacGAP has well-documented scaffolding functions, whether it influences Pav/kinesin-6 function is less well-explored. This study demonstrates that both Pav/kinesin-6 and the centralspindlin complex (co-expressed Pav/Tum) have strong microtubule bundling activity. Centralspindlin also has robust plus-end-directed motility. In contrast, Pav/kinesin-6 alone cannot move microtubules. However, the addition of Tum/RacGAP or a 65 amino acid Tum/RacGAP fragment to Pav/kinesin-6 restores microtubule motility. Further, ATPase assays reveal that microtubule-stimulated ATPase activity of centralspindlin is seven times higher than that of Pav/kinesin-6. These findings are supported by in vivo studies demonstrating that in Tum/RacGAP-depleted S2 Drosophila cells, Pav/kinesin-6 exhibits severely reduced localization to the central spindle and an abnormal concentration at the centrosomes.

Ye, A. A., Deretic, J., Hoel, C. M., Hinman, A. W., Cimini, D., Welburn, J. P. and Maresca, T. J. (2015). Aurora A kinase contributes to a pole-based error correction pathway. Curr Biol 25: 1842-1851. PubMed ID: 26166783 Summary: Chromosome biorientation, where sister kinetochores attach to microtubules (MTs) from opposing spindle poles, is the configuration that best ensures equal partitioning of the genome during cell division. Erroneous kinetochore-MT attachments are commonplace but are often corrected prior to anaphase. Error correction, thought to be mediated primarily by the centromere-enriched Aurora B kinase (ABK), typically occurs near spindle poles; however, the relevance of this locale is unclear. Furthermore, polar ejection forces (PEFs), highest near poles, can stabilize improper attachments by pushing mal-oriented chromosome arms away from spindle poles. Hence, there is a conundrum: erroneous kinetochore-MT attachments are weakened where PEFs are most likely to strengthen them. This study reports that Aurora A kinase (AAK) opposes the stabilizing effect of PEFs. AAK activity contributes to phosphorylation of kinetochore substrates near poles and its inhibition results in chromosome misalignment and an increased incidence of erroneous kinetochore-MT attachments. Furthermore, AAK directly phosphorylates a site in the N-terminal tail of Ndc80/Hec1 that has been implicated in reducing the affinity of the Ndc80 complex for MTs when phosphorylated. It is proposed that an AAK activity gradient contributes to correcting mal-oriented kinetochore-MT attachments in the vicinity of spindle poles.

Eisman, R. C., Phelps, M. A. and Kaufman, T. C. (2016). The End of a Monolith: Deconstructing the Cnn-Polo interaction. Fly (Austin): [Epub ahead of print]. PubMed ID: 27096551 Summary: In Drosophila melanogaster a functional pericentriolar matrix (PCM) at mitotic centrosomes requires Centrosomin-Long Form (Cnn-LF) proteins. Moreover, tissue culture cells have shown that the centrosomal localization of both Cnn-LF and Polo kinase are co-dependent, suggesting a direct interaction. A recent study found Cnn potentially binds to and is phosphorylated by Polo kinase at two residues encoded by Exon1A, the initiating exon of a subset of Cnn isoforms. These interactions are required for the centrosomal localization of Cnn-LF in syncytial embryos and a mutation of either phosphorylation site is sufficient to block localization of both mutant and wild-type Cnn when they are co-expressed. Immunoprecipitation experiments show that Cnn-LF interacts directly with mitotically activated Polo kinase and requires the two phosphorylation sites in Exon1A. These IP experiments also show that Cnn-LF proteins form multimers. Depending on the stoichiometry between functional and mutant peptides, heteromultimers exhibit dominant negative or positive trans-complementation (rescue) effects on mitosis. Additionally, following the completion of meiosis, Cnn-Short Form (Cnn-SF) proteins are required for polar body formation in embryos, a process previously shown to require Polo kinase. These findings, when combined with previous work, clearly demonstrate the complexity of cnn and show that a view of cnn as encoding a single peptide is too simplistic.

Thursday, May 5th

Chaubal, A., Todi, S.V. and Pile, L.A. (2016). Inter-isoform-dependent regulation of the Drosophila master transcriptional regulator SIN3. J Biol Chem [Epub ahead of print]. PubMed ID: 27129248 Summary: SIN3 is a transcriptional corepressor that acts as a scaffold for a histone deacetylase (HDAC) complex. The SIN3 complex regulates various biological processes, including organ development, cell proliferation and energy metabolism. Little is known, however, about the regulation of SIN3 itself. There are two major isoforms of Drosophila SIN3, 187 and 220, which are differentially expressed. Intrigued by the developmentally timed exchange of SIN3 isoforms, this study examined whether SIN3 187 controls the fate of the 220 counterpart. It was shown that in developing tissue there is interplay between SIN3 isoforms: when SIN3 187 protein levels increase, SIN3 220 protein decreases concomitantly. SIN3 187 has a dual effect on SIN3 220. Expression of 187 leads to reduced 220 transcript, while also increasing the turnover of SIN3 220 protein by the proteasome. These data support the presence of a novel, inter-isoform-dependent mechanism that regulates the amount of SIN3 protein, and potentially the level of specific SIN3 complexes, during distinct developmental stages.

Coulthard, A. B., Taylor-Kamall, R. W., Hallson, G., Axentiev, A., Sinclair, D. A., Honda, B. M. and Hilliker, A. J. (2016). Meiotic recombination is suppressed near the histone-defined border of euchromatin and heterochromatin on chromosome 2L of Drosophila melanogaster. Genome 59: 289-294. PubMed ID: 27031007 Summary: In Drosophila melanogaster, the borders between pericentric heterochromatin and euchromatin on the major chromosome arms have been defined in various ways, including chromatin-specific histone modifications, the binding patterns of heterochromatin-enriched chromosomal proteins, and various cytogenetic techniques. Elucidation of the genetic properties that independently define the different chromatin states associated with heterochromatin and euchromatin should help refine the boundary. Since meiotic recombination is present in euchromatin, but absent in heterochromatin, it constitutes a key genetic property that can be observed transitioning between chromatin states. Using P element insertion lines marked with a su(Hw) insulated mini-white gene, meiotic recombination was found to transition in a region consistent with the H3K9me2 transition observed in ovaries.

Ramachandran, S. and Henikoff, S. (2016). Transcriptional regulators compete with nucleosomes post-replication. Cell 165: 580-592. PubMed ID: 27062929 Summary: Every nucleosome across the genome must be disrupted and reformed when the replication fork passes, but how chromatin organization is re-established following replication is unknown. To address this problem, Mapping In vivo Nascent Chromatin with EdU and sequencing (MINCE-seq) was developed to characterize the genome-wide location of nucleosomes and other chromatin proteins behind replication forks at high temporal and spatial resolution. The characteristic chromatin landscape at Drosophila promoters and enhancers is lost upon replication. The most conspicuous changes are at promoters that have high levels of RNA polymerase II (RNAPII) stalling and DNA accessibility and show specific enrichment for the BRM remodeler. Enhancer chromatin is also disrupted during replication, suggesting a role for transcription factor (TF) competition in nucleosome re-establishment. Thus, the characteristic nucleosome landscape emerges from a uniformly packaged genome by the action of TFs, RNAPII, and remodelers minutes after replication fork passage.

Li, H. B., Ohno, K., Gui, H. and Pirrotta, V. (2013). Insulators target active genes to transcription factories and polycomb-repressed genes to polycomb bodies. PLoS Genet 9: e1003436. PubMed ID: 23637616 Summary: Polycomb bodies are foci of Polycomb proteins in which different Polycomb target genes are thought to co-localize in the nucleus, looping out from their chromosomal context. WInsulators, not Polycomb response elements (PREs), have been shown to mediate associations among Polycomb Group (PcG) targets to form Polycomb bodies. This study used live imaging and 3C interactions to show that transgenes containing PREs and endogenous PcG-regulated genes are targeted by insulator proteins to different nuclear structures depending on their state of activity. When two genes are repressed, they co-localize in Polycomb bodies. When both are active, they are targeted to transcription factories in a fashion dependent on Trithorax and enhancer specificity as well as the insulator protein CTCF. In the absence of CTCF, assembly of Polycomb bodies is essentially reduced to those representing genomic clusters of Polycomb target genes. The critical role of Trithorax suggests that stable association with a specialized transcription factory underlies the cellular memory of the active state.

Wednesday, May 4th

Jaiswal, M., Haelterman, N. A., Sandoval, H., Xiong, B., Donti, T., Kalsotra, A., Yamamoto, S., Cooper, T. A., Graham, B. H. and Bellen, H. J. (2015). Impaired mitochondrial energy production causes light-induced photoreceptor degeneration independent of oxidative stress. PLoS Biol 13: e1002197. PubMed ID: 26176594 Summary: In an unbiased forward genetic screen designed to isolate mutations that cause photoreceptor degeneration, mutations were identified in a nuclear-encoded mitochondrial gene, ppr, a homolog of human LRPPRC. ppr was found to be required for protection against light-induced degeneration. Its function is essential to maintain membrane depolarization of the photoreceptors upon repetitive light exposure, and an impaired phototransduction cascade in ppr mutants results in excessive Rhodopsin1 endocytosis. Moreover, loss of ppr results in a reduction in mitochondrial RNAs, reduced electron transport chain activity, and reduced ATP levels. Oxidative stress, however, is not induced. It is proposed that the reduced ATP level in ppr mutants underlies the phototransduction defect, leading to increased Rhodopsin1 endocytosis during light exposure, causing photoreceptor degeneration independent of oxidative stress. This hypothesis is bolstered by characterization of two other genes isolated in the screen, pyruvate dehydrogenase and citrate synthase. Their loss also causes a light-induced degeneration, excessive Rhodopsin1 endocytosis and reduced ATP without concurrent oxidative stress, unlike many other mutations in mitochondrial genes that are associated with elevated oxidative stress and light-independent photoreceptor demise.

Ruan, W., Srinivasan, A., Lin, S., Kara, K. I. and Barker, P. A. (2016). Eiger-induced cell death relies on Rac1-dependent endocytosis. Cell Death Dis 7: e2181. PubMed ID: 27054336 Summary: Signaling via tumor necrosis factor receptor (TNFR) superfamily members regulates cellular life and death decisions. A subset of mammalian TNFR proteins, most notably the p75 neurotrophin receptor (p75NTR), induces cell death through a pathway that requires activation of c-Jun N-terminal kinases (JNKs). However the receptor-proximal signaling events that mediate this remain unclear. Drosophila express a single tumor necrosis factor (TNF) ligand termed Eiger (Egr) that activates JNK-dependent cell death. This model was exploited to identify phylogenetically conserved signaling events that allow Egr to induce JNK activation and cell death in vivo. This study reports that Rac1, a small GTPase, is specifically required in Egr-mediated cell death. rac1 loss of function blocks Egr-induced cell death, whereas Rac1 overexpression enhances Egr-induced killing. Vav was identified as a GEF for Rac1 in this pathway, and dLRRK functions were identified as a negative regulator of Rac1 that normally acts to constrain Egr-induced death. Thus dLRRK loss of function increases Egr-induced cell death in the fly. Rac1-dependent entry of Egr into early endosomes was shown to be a crucial prerequisite for JNK activation and for cell death and show that this entry requires the activity of Rab21 and Rab7. These findings reveal novel regulatory mechanisms that allow Rac1 to contribute to Egr-induced JNK activation and cell death.

Huang, Z., Ren, S., Jiang, Y. and Wang, T. (2016). PINK1 and Parkin cooperatively protect neurons against constitutively active TRP channel-induced retinal degeneration in Drosophila. Cell Death Dis 7: e2179. PubMed ID: 27054334 Summary: Calcium has an important role in regulating numerous cellular activities. However, extremely high levels of intracellular calcium can lead to neurotoxicity, a process commonly associated with degenerative diseases. Despite the clear role of calcium cytotoxicity in mediating neuronal cell death in this context, the pathological mechanisms remain controversial. This study used a well-established Drosophila model of retinal degeneration, which involves the constitutively active TRPP365 channels, to study calcium-induced neurotoxicity. Disruption of mitochondrial function was found to be associated with the degenerative process. Further, increasing autophagy flux prevented cell death in TrpP365PINK1/Parkin pathway. In addition, the retinal degeneration process was also suppressed by the coexpression of PINK1 and Parkin. These results provide genetic evidence that mitochondrial dysfunction has a key role in the pathology of cellular calcium neurotoxicity. In addition, the results demonstrated that maintaining mitochondrial homeostasis via PINK1/Parkin-dependent mitochondrial quality control can potentially alleviate cell death in a wide range of neurodegenerative diseases.

Lee, T. V., Kamber Kaya, H. E., Simin, R., Baehrecke, E. H. and Bergmann, A. (2016). The initiator caspase Dronc is subject of enhanced autophagy upon proteasome impairment in Drosophila. Cell Death Differ [Epub ahead of print]. PubMed ID: 27104928 Summary: A major function of ubiquitylation is to deliver target proteins to the proteasome for degradation. In the apoptotic pathway in Drosophila, the inhibitor of apoptosis protein 1 (Diap1) regulates the activity of the initiator caspase Dronc (death regulator Nedd2-like caspase; caspase-9 ortholog) by ubiquitylation, supposedly targeting Dronc for degradation by the proteasome. Using a genetic approach, this study showed that Dronc protein fails to accumulate in epithelial cells with impaired proteasome function suggesting that it is not degraded by the proteasome, contrary to the expectation. Similarly, decreased autophagy, an alternative catabolic pathway, does not result in increased Dronc protein levels. However, combined impairment of the proteasome and autophagy triggers accumulation of Dronc protein levels suggesting that autophagy compensates for the loss of the proteasome with respect to Dronc turnover. Consistently, it was shown that loss of the proteasome enhances endogenous autophagy in epithelial cells. It is proposed that enhanced autophagy degrades Dronc if proteasome function is impaired.

Tuesday, May 3rd

Croy, H. E., et al. (2016). The PARP enzyme Tankyrase antagonizes activity of the β-catenin destruction complex through ADP-ribosylation of Axin and APC2. J Biol Chem [Epub ahead of print]. PubMed ID: 27068743 Summary: Most colon cancer cases are initiated by truncating mutations in APC. APC is a critical negative regulator of the Wnt signaling pathway that participates in a multi-protein destruction complex to target the key effector protein βcatenin for proteolysis. Poly ADP-ribose Polymerase (PARP) enzyme Tankyrase (TNKS) has been shown antagonizes destruction complex activity by promoting degradation of the scaffold protein Axin. A yeast two-hybrid (Y2H) screen uncovered TNKS as a putative binding partner of Drosophila APC2, suggesting that TNKS may play multiple roles in destruction complex regulation. TNKS was found to bind a C-terminal RPQPSG motif in Drosophila APC2, and that this motif is conserved in human APC2, but not human APC1. In addition, APC2 can recruit TNKS into the βcatenin destruction complex, placing the APC2/TNKS interaction at the correct intracellular location to regulate βcatenin proteolysis. TNKS directly PARylates both Drosophila Axin and APC2, but that PARylation does not globally regulate APC2 protein levels as it does for Axin. Moreover, TNKS inhibition in colon cancer cells decreases βcatenin signaling, which cannot be explained solely through Axin stabilization. Instead, these findings suggest that TNKS regulates destruction complex activity at the level of both Axin and APC2, providing further mechanistic insight into TNKS inhibition as a potential Wnt pathway cancer therapy.

Satoh, T., Nakamura, Y. and Satoh, A.K. (2016). Rab6 functions in polarized transport in Drosophila photoreceptors. Fly (Austin) [Epub ahead of print]. PubMed ID: 27116570 Summary: Selective membrane transport pathways are essential for cells in situ to construct and maintain a polarized structure comprising multiple plasma membrane domains, which is essential for their specific cellular functions. Genetic screening in Drosophila photoreceptors harboring multiple plasma membrane domains enables the identification of genes involved in polarized transport pathways. This study performed genome-wide high-throughput screening and identified a Rab6-null mutant with a rare phenotype characterized by a loss of 2 apical transport pathways with an intact basolateral transport. Although the functions of Rab6 in the Golgi apparatus are well known, its function in polarized transport is unexpected. The mutant phenotype and localization of Rab6 strongly indicate that Rab6 regulates transport between the trans-Golgi network (TGN) and recycling endosomes (REs): basolateral cargos are segregated at the TGN before Rab6 functions, but cargos going to multiple apical domains are sorted at REs. Both the medial-Golgi resident protein MPPE and the TGN marker GalT::CFP exhibit diffused co-localized distributions in Rab6-deficient cells, suggesting they are trapped in the retrograde transport vesicles returning to trans-Golgi cisternae. Hence, the study proposes that Rab6 regulates the fusion of retrograde transport vesicles containing medial, trans-Golgi resident proteins to the Golgi cisternae, which causes Golgi maturation to REs.

Deshpande, G., Manry, D., Jourjine, N., Mogila, V., Mozes, H., Bialistoky, T., Gerlitz, O. and Schedl, P. (2016). Functioning of an ABC transporter, Mdr49, in Hh signaling and germ cell migration. Development [Epub ahead of print]. PubMed ID: 27122170 Summary: Coalescence of the embryonic gonad in Drosophila melanogaster requires directed migration of the primordial germ cells (PGCs) towards the somatic gonadal precursor cells (SGPs). It has been recently proposed that an ATP-Binding Cassette (ABC) transporter, Mdr49, functions in the embryonic mesoderm to facilitate the transmission of the PGC attractant from the SGPs; however, the precise molecular identity of the mdr49 dependent guidance signal remains elusive. Employing the 'loss' and 'gain' of function strategies, this study shows that mdr49 is a component of the Hedgehog pathway and it potentiates the signaling activity. This function is direct as, in mdr49 mutant embryos, Hh ligand is inappropriately sequestered in the hh expressing cells. Data also suggest that role of Mdr49 is to provide cholesterol for the correct processing of the Hh precursor protein. Supporting this conclusion, PGC migration defects in mdr49 embryos are substantially ameliorated by a cholesterol-rich diet.

Agrawal, N., Delanoue, R., Mauri, A., Basco, D., Pasco, M., Thorens, B. and Leopold, P. (2016). The Drosophila TNF Eiger is an adipokine that acts on insulin-producing cells to mediate nutrient response. Cell Metab 23: 675-684. PubMed ID: 27076079 Summary: Adaptation of organisms to ever-changing nutritional environments relies on sensor tissues and systemic signals. Identification of these signals would help understand the physiological crosstalk between organs contributing to growth and metabolic homeostasis. This study shows that Eiger, the Drosophila TNF-alpha, is a metabolic hormone that mediates nutrient response by remotely acting on insulin-producing cells (IPCs). In the condition of nutrient shortage, a metalloprotease of the TNF-alpha converting enzyme (TACE) family is active in fat body (adipose-like) cells, allowing the cleavage and release of adipose Eiger in the hemolymph. In the brain IPCs, Eiger activates its receptor Grindelwald, leading to JNK-dependent inhibition of insulin production. Therefore, this study has identified a humoral connexion between the fat body and the brain insulin-producing cells relying on TNF-alpha that mediates adaptive response to nutrient deprivation.

Monday, May 2

Bivik, C., MacDonald, R. B., Gunnar, E., Mazouni, K., Schweisguth, F. and Thor, S. (2016) . Control of neural daughter cell proliferation by multi-level Notch/Su(H)/E(spl)-HLH signaling. PLoS Genet 12: e1005984. PubMed ID: 27070787 Summary: The Notch pathway controls proliferation during development and in adulthood, and is frequently affected in many disorders. However, the genetic sensitivity and multi-layered transcriptional properties of the Notch pathway has made its molecular decoding challenging. This study addresses the complexity of Notch signaling with respect to proliferation, using the developing Drosophila CNS as model. A Notch/Su(H)/E(spl)-HLH cascade was found to specifically controls daughter, but not progenitor proliferation. Additionally, it was found that different E(spl)-HLH genes are required in different neuroblast lineages. The Notch/Su(H)/E(spl)-HLH cascade alters daughter proliferation by regulating four key cell cycle factors: Cyclin E, String/Cdc25, E2f and Dacapo (mammalian p21CIP1/p27KIP1/p57Kip2). ChIP and DamID analysis of Su(H) and E(spl)-HLH indicates direct transcriptional regulation of the cell cycle genes, and of the Notch pathway itself. These results point to a multi-level signaling model and may help shed light on the dichotomous proliferative role of Notch signaling in many other systems.

Corty, M.M., Tam, J. and Grueber, W.B. (2016). Dendritic diversification through transcription factor-mediated suppression of alternative morphologies. Development 143: 1351-1362. PubMed ID: 27095495 Summary: Neurons display a striking degree of functional and morphological diversity, and the developmental mechanisms that underlie diversification are of significant interest for understanding neural circuit assembly and function. This study finds that the morphology of Drosophila sensory neurons is diversified through a series of suppressive transcriptional interactions involving the POU domain transcription factors Pdm1 (Nubbin) and Pdm2, the homeodomain transcription factor Cut, and the transcriptional regulators Scalloped and Vestigial. Pdm1 and Pdm2 are expressed in a subset of proprioceptive sensory neurons and function to inhibit dendrite growth and branching. A subset of touch receptors show a capacity to express Pdm1/2, but Cut represses this expression and promotes more complex dendritic arbors. Levels of Cut expression are diversified in distinct sensory neurons by selective expression of Scalloped and Vestigial. Different levels of Cut impact dendritic complexity and, consistent with this, it was found that Scalloped and Vestigial suppress terminal dendritic branching. This transcriptional hierarchy therefore acts to suppress alternative morphologies to diversify three distinct types of somatosensory neurons.

Peng, Q., Wang, Y., Li, M., Yuan, D., Xu, M., Li, C., Gong, Z., Jiao, R. and Liu, L. (2016). cGMP-dependent protein kinase encoded by foraging regulates motor axon guidance in Drosophila by suppressing Lola function. J Neurosci 36: 4635-4646. PubMed ID: 27098704 Summary: Correct pathfinding and target recognition of a developing axon are exquisitely regulated processes that require multiple guidance factors. Among these factors, the second messengers, cAMP and cGMP, are known to be involved in establishing the guidance cues for axon growth through different intracellular signaling pathways. However, whether and how cGMP-dependent protein kinase (PKG) regulates axon guidance remains poorly understood. This study shows that the motor axons of intersegmental nerve b (ISNb) in the Drosophila embryo display targeting defects during axon development in the absence of foraging (for), a gene encoding PKG. In vivo tag expression reveals PKG to be present in the ventral nerve code at late embryonic stages, supporting its function in embryonic axon guidance. Mechanistic studies show that the transcription factor longitudinal lacking (lola) genetically interacts with for. PKG physically associates with the LolaT isoform via the C-terminal zinc-finger-containing domain. Overexpression of PKG leads to the cytoplasmic retention of LolaT in S2 cells, suggesting a role for PKG in mediating the nucleocytoplasmic trafficking of Lola. Together, these findings reveal a novel function of PKG in regulating the establishment of neuronal connectivity by sequestering Lola in the cytoplasm.

Urbach, R., Jussen, D. and Technau, G.M. (2016). Gene expression profiles uncover individual identities of gnathal neuroblasts and serial homologies in the embryonic CNS of Drosophila. Development 143: 1290-1301. PubMed ID: 27095493 Summary: This study constructed comprehensive neuroblast maps for the three gnathal head segments. Based on the spatiotemporal pattern of neuroblast formation and the expression profiles of 46 marker genes (41 transcription factors), each neuroblast can be uniquely identified. Compared with the thoracic ground state, neuroblast numbers are progressively reduced in labial, maxillary and mandibular segments due to smaller sizes of neuroectodermal anlagen and, partially, to suppression of neuroblast formation and induction of programmed cell death by the Hox gene Deformed. Neuroblast patterns are further influenced by segmental modifications in dorsoventral and proneural gene expression. With the previously published neuroblast maps and those presented here for the gnathal region, all neuroectodermal neuroblasts building the CNS of the fly (ventral nerve cord and brain, except optic lobes) are now individually identified (in total 2×567 neuroblasts). This allows, for the first time, a comparison of the characteristics of segmental populations of stem cells and to screen for serially homologous neuroblasts throughout the CNS. It was found that approximately half of the deutocerebral and all of the tritocerebral (posterior brain) and gnathal neuroblasts, but none of the protocerebral (anterior brain) neuroblasts, display serial homology to neuroblasts in thoracic/abdominal neuromeres. Modifications in the molecular signature of serially homologous neuroblasts are likely to determine the segment-specific characteristics of their lineages.

Sunday, May 1st

Rosin, L. and Mellone, B.G. (2016). Co-evolving CENP-A and CAL1 domains mediate centromeric CENP-A deposition across Drosophila species. Dev Cell 37: 136-147. PubMed ID: 27093083 Summary: Centromeres mediate the conserved process of chromosome segregation, yet centromeric DNA and the centromeric histone, CENP-A, are rapidly evolving. The rapid evolution of Drosophila CENP-A loop 1 (L1) is thought to modulate the DNA-binding preferences of CENP-A to counteract centromere drive, the preferential transmission of chromosomes with expanded centromeric satellites. Consistent with this model, CENP-A from Drosophila bipectinata (bip) cannot localize to Drosophila melanogaster (mel) centromeres. It was shown that this result is due to the inability of the mel CENP-A chaperone, CAL1, to deposit bip CENP-A into chromatin. Co-expression of bip CENP-A and bip CAL1 in mel cells restores centromeric localization, and similar findings apply to other Drosophila species. Two co-evolving regions, CENP-A L1 and the CAL1 N terminus, were identified as critical for lineage-specific CENP-A incorporation. Collectively, these data show that the rapid evolution of L1 modulates CAL1-mediated CENP-A assembly, suggesting an alternative mechanism for the suppression of centromere drive.

Webb, A. E., Kundaje, A. and Brunet, A. (2016). Characterization of the direct targets of FOXO transcription factors throughout evolution. Aging Cell [Epub ahead of print]. PubMed ID: 27061590 Summary: FOXO transcription factors (FOXOs) are central regulators of lifespan across species, yet they also have cell-specific functions, including adult stem cell homeostasis and immune function. Whether FOXO targets are specific to cell types and species or conserved across cell types and throughout evolution remains uncharacterized. This study consisted of a analysis of direct FOXO targets across tissues and organisms, using data from mammals as well as C. elegans and Drosophila. FOXOs were shown to bind cell type-specific targets, which have functions related to that particular cell. Interestingly, FOXOs also share targets across different tissues in mammals, and the function and even the identity of these shared mammalian targets are conserved in invertebrates. Evolutionarily conserved targets show enrichment for growth factor signaling, metabolism, stress resistance, and proteostasis, suggesting an ancestral, conserved role in the regulation of these processes. Candidate cofactors at conserved FOXO targets were identified that change in expression with age, including CREB and ETS family factors. This analysis provides insight into the evolution of the FOXO network and highlights downstream genes and cofactors that may be important for FOXO's conserved function in adult homeostasis and longevity.

Kim, J. H., Kim, S. K., Lee, J. H., Kim, Y. J., Goddard, W. A. and Kim, Y. C. (2016). Homology modeling and molecular docking studies of Drosophila and Aedes sex peptide receptors. J Mol Graph Model 66: 115-122. PubMed ID: 27060892 Summary: The Drosophila melanogaster Sex peptide receptor (DrmSPR), a G protein-coupled receptor (GPCR), is known as the specific receptor for sex peptide (SP). It is responsible for the reproductive behavior in the Drosophila model system; in particular, it is involved in the post-mating responses such as the increase in egg-laying ability and decrease in receptivity in females. A previous studydiscovered a small molecule agonist of DrmSPR which could not, however, activate Aedes aegypti SPR (AedesSPR). To investigate the binding mechanism of the small molecule agonist of DrmSPR, the ensemble structures of low-lying packing structures of DrmSPR and AedesSPR were assembled using the GEnSeMBLE (GPCR Ensemble of Structures in Membrane BiLayer Environment) method. The generated homology models exhibited the typical pattern of inter-helical interactions of the class A GPCRs. The docking experiments of the small molecule agonist suggest that Tyr5.35 and Phe2.67 residues may be involved in a hydrophobic interaction and that Ser3.25 forms a hydrogen bond with the agonist. Additionally, the docking results were found to be consistent with the experimental data of the reference compounds with variable agonistic activities. Moreover, a potential distinction of the putative binding sites in two GPCR models of DrmSPR and AedesSPR, which was determined in this study, can explain the selective action of the agonist for DrmSPR but not for AedesSPR.

Kriesner, P., Conner, W. R., Weeks, A. R., Turelli, M. and Hoffmann, A. A. (2016). Persistence of a Wolbachia infection frequency cline in Drosophila melanogaster and the possible role of reproductive dormancy. Evolution [Epub ahead of print]. PubMed ID: 27076356 Summary: Field populations of arthropods are often polymorphic for Wolbachia but the factors maintaining intermediate Wolbachia frequencies are generally not understood. In Drosophila melanogaster, Wolbachia frequencies are highly variable across the globe. This study documented the persistence of a Wolbachia infection frequency cline in D. melanogaster populations from eastern Australia across at least 20 years, with frequencies generally high in the tropics but lower in cool temperate regions. The results are interpreted using a model of frequency dynamics incorporating cytoplasmic incompatibility, imperfect maternal transmission and Wolbachia effects on fitness. Clinal variation is less pronounced in eastern North America which may reflect annual recolonization at higher latitudes. Limited samples from Africa from latitudes matching the tropical and subtropical samples from Australia and North America show comparably high infection frequencies, but some equatorial samples show lower frequencies. Adult dormancy across cold periods may contribute to the Australian Wolbachia cline. Infected flies exposed to cold conditions for an extended period had reduced fecundity and viability, an effect not evident in unexposed controls. These fitness costs may contribute to the relatively low Wolbachia frequencies in Australian temperate areas; whereas different processes, including cytoplasmic incompatibility induced by young males, may contribute to higher frequencies in tropical locations.

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