What's hot today:
Current papers in developmental biology and gene function


Friday, March 24th

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Duan, Y., Dou, S., Luo, S., Zhang, H. and Lu, J. (2017). Adaptation of A-to-I RNA editing in Drosophila. PLoS Genet 13(3): e1006648. PubMed ID: 28282384
Adenosine-to-inosine (A-to-I) editing, catalyzed by adenosine deaminase acting on RNA (ADAR), is hypothesized to facilitate adaptive evolution by expanding proteomic diversity through an epigenetic approach. However, it is challenging to provide evidences to support this hypothesis at the whole editome level. This study systematically characterized 2,114 A-to-I RNA editing sites in female and male brains of D. melanogaster, and nearly half of these sites had events evolutionarily conserved across Drosophila species. Strong signatures were detected of positive selection on the nonsynonymous editing sites in Drosophila brains, and the beneficial editing sites were significantly enriched in genes related to chemical and electrical neurotransmission. The signal of adaptation was even more pronounced for the editing sites located in X chromosome or for those commonly observed across Drosophila species. A set of gene candidates (termed "PSEB" genes) was identified that had nonsynonymous editing events favored by natural selection. Evidence is presented that editing preferentially increased mutation sequence space of evolutionarily conserved genes, which supported the adaptive evolution hypothesis of editing. Prevalent nonsynonymous editing sites were found that were favored by natural selection in female and male adults from five strains of D. melanogaster. Temperature played a more important role than gender effect in shaping the editing levels, although the effect of temperature is relatively weaker compared to that of species effect. The relevant factors were explored that shape the selective patterns of the global editomes. Altogether this study demonstrated that abundant nonsynonymous editing sites in Drosophila brains were adaptive and maintained by natural selection during evolution. These results shed new light on the evolutionary principles and functional consequences of RNA editing.
Sato, A., Suematsu, T., Aihara, K. K., Kita, K., Suzuki, T., Watanabe, K., Ohtsuki, T. and Watanabe, Y. I. (2017). Duplication of Drosophila melanogaster mitochondrial EF-Tu: pre-adaptation to T-arm truncation and exclusion of bulky aminoacyl residues. Biochem J [Epub ahead of print]. PubMed ID: 28130490
Evolutionary Homolog Study
Translation elongation factor Tu (EF-Tu) delivers aminoacyl-tRNA to ribosomes in protein synthesis. EF-Tu generally recognizes aminoacyl moieties and acceptor- and T-stems of aminoacyl-tRNAs. However, nematode mitochondrial (mt) tRNAs frequently lack all or part of the T-arm that is recognized by canonical EF-Tu. It has been reported that two distinct EF-Tu species, EF-Tu1 and EF-Tu2, respectively recognize mt tRNAs lacking T-arms and D-arms in the mitochondria of the chromadorean nematode C. elegans. C. elegans EF-Tu2 specifically recognizes the seryl-moiety of serylated D-armless tRNAs. Mitochondria of the enoplean nematode Trichinella possess three structural types of tRNAs: T-armless tRNAs, D-armless tRNAs, and cloverleaf tRNAs with a short T-arm. Trichinella mt EF-Tu1 binds to all three types and EF-Tu2 binds only to D-armless Ser-tRNAs, showing an evolutionary intermediate state from canonical EF-Tu to chromadorean nematode (e.g. C. elegans) EF-Tu species. This study reports that two EF-Tu species also participate in Drosophila mitochondria. Both Drosophila EF-Tu1 and EF-Tu2 bound to cloverleaf and D-armless tRNAs. Drosophila EF-Tu1 has the ability to recognize T-armless tRNAs that do not evidently exist in Drosophila mitochondria but do exist in related arthropod species. In addition, Drosophila EF-Tu2 preferentially bound to aa-tRNAs carrying small amino acids, but not to aa-tRNAs carrying bulky amino acids. These results suggest that the Drosophila mitochondrial translation system could be another intermediate state between the canonical and nematode mitochondria-type translation systems.
Zhang, R., Deng, P., Jacobson, D. and Li, J. B. (2017). Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing. PLoS Genet 13(2): e1006563. PubMed ID: 28166241
Adenosine-to-inosine RNA editing, catalyzed by adenosine deaminase acting on RNA (ADAR), diversifies the transcriptome and promotes functional diversity, particularly in the brain. A plethora of editing sites has been recently identified; however, how they are selected and regulated and which are functionally important are largely unknown. This study shows the cis-regulation and stepwise selection of RNA editing during Drosophila evolution and pinpoints a large number of functional editing sites. Establishment of editing and variation in editing levels across Drosophila species were found to be largely explained and predicted by cis-regulatory elements. Furthermore, editing events that arose early in the species tree tend to be more highly edited in clusters and enriched in slowly-evolved neuronal genes, thus suggesting that the main role of RNA editing is for fine-tuning neurological functions. While nonsynonymous editing events have been long recognized as playing a functional role, in addition to nonsynonymous editing sites, a large fraction of 3'UTR editing sites is evolutionarily constrained, highly edited, and thus likely functional. These 3'UTR editing events can alter mRNA stability and affect miRNA binding and thus highlight the functional roles of noncoding RNA editing. This work, through evolutionary analyses of RNA editing in Drosophila, uncovers novel insights of RNA editing regulation as well as its functions in both coding and non-coding regions.
Obayashi, E., et al. (2017). Molecular landscape of the ribosome pre-initiation complex during mRNA scanning: Structural role for eIF3c and its control by eIF5. Cell Rep 18(11): 2651-2663. PubMed ID: 28297669
Evolutionary Homolog Study
During eukaryotic translation initiation factor, eIF3 binds the solvent-accessible side of the 40S ribosome and recruits the gate-keeper protein eIF1 (see Drosophila eIF1) and eIF5 (see Drosophila eIF5) to the decoding center. This is largely mediated by the N-terminal domain (NTD) of eIF3c (see Drosophila eIF3c), which can be divided into three parts: 3c0, 3c1, and 3c2. The N-terminal part, 3c0, binds eIF5 strongly but only weakly to the ribosome-binding surface of eIF1, whereas 3c1 and 3c2 form a stoichiometric complex with eIF1. 3c1 contacts eIF1 through Arg-53 and Leu-96, while 3c2 faces 40S protein uS15/S13, to anchor eIF1 to the scanning pre-initiation complex (PIC). It is proposed that the 3c0:eIF1 interaction diminishes eIF1 binding to the 40S, whereas 3c0:eIF5 interaction stabilizes the scanning PIC by precluding this inhibitory interaction. Upon start codon recognition, interactions involving eIF5, and ultimately 3c0:eIF1 association, facilitate eIF1 release. These results, carried out with S. cerevisiae proteins, reveal intricate molecular interactions within the PIC, programmed for rapid scanning-arrest at the start codon.
Shan, L., Wu, C., Chen, D., Hou, L., Li, X., Wang, L., Chu, X., Hou, Y. and Wang, Z. (2017). Regulators of alternative polyadenylation operate at the transition from mitosis to meiosis. J Genet Genomics [Epub ahead of print]. PubMed ID: 28190776
n the sexually reproductive organisms, gametes are produced by meiosis following a limited mitotic amplification. However, the intrinsic program switching cells from mitotic to meiotic cycle is unclear. Alternative polyadenylation (APA) is a highly conserved means of gene regulation and is achieved by the RNA 3'-processing machinery to generate diverse 3'UTR profiles. In Drosophila spermatogenesis, this study observed distinct profiles of transcriptome-wide 3'UTR between mitotic and meiotic cells. In mutant germ cells stuck in mitosis, 3'UTRs of hundreds of genes were consistently shifted. Remarkably, altering the levels of multiple 3'-processing factors disrupted germline's progression to meiosis, indicative of APA's active role in this transition. An RNA-binding protein (RBP) Tut could directly bind 3'UTRs of 3'-processing factors whose expressions were repressed in the presence of Tut-containing complex. Further, this RBP complex could execute the repression post-transcriptionally by recruiting CCR4/Twin of deadenylation complex. Thus, it is proposed that an RBP complex regulates the dynamic APA profile to promote the mitosis-to-meiosis transition.
Wang, L., Nam, Y., Lee, A. K., Yu, C., Roth, K., Chen, C., Ransey, E. M. and Sliz, P. (2017). LIN28 zinc knuckle domain is required and sufficient to induce let-7 oligouridylation. Cell Rep 18(11): 2664-2675. PubMed ID: 28297670
Evolutionary Homolog Study
LIN28 (see Drosophila Lin28) is an RNA binding protein that plays crucial roles in pluripotency, glucose metabolism, tissue regeneration, and tumorigenesis. LIN28 binds to the let-7 (see Drosophila let-7) primary and precursor microRNAs through bipartite recognition and induces degradation of let-7 precursors (pre-let-7) by promoting oligouridylation by terminal uridylyltransferases (TUTases; see Drosophila Tailor). This study report that the zinc knuckle domain (ZKD) of mouse LIN28 recruits TUT4 to initiate the oligouridylation of let-7 precursors. Crystal structure of human LIN28 in complex with a fragment of pre-let-7f-1 determined to 2.0 Å resolution shows that the interaction between ZKD and RNA is constrained to a small cavity with a high druggability score. The specific interaction between ZKD and pre-let-7 was shown to be necessary and sufficient to induce oligouridylation by recruiting the N-terminal fragment of TUT4 (NTUT4) and the formation of a stable ZKD:NTUT4:pre-let-7 ternary complex is crucial for the acquired processivity of TUT4.

Thursday, March 23rd

Fisher, Y. E., Yang, H. H., Isaacman-Beck, J., Xie, M., Gohl, D. M. and Clandinin, T. R. (2017). FlpStop, a tool for conditional gene control in Drosophila. Elife 6. PubMed ID: 28211790
Manipulating gene function cell type-specifically is a common experimental goal in Drosophila research and has been central to studies of neural development, circuit computation, and behavior. However, current cell type-specific gene disruption techniques in flies often reduce gene activity incompletely or rely on cell division. This study describes FlpStop, a generalizable tool for conditional gene disruption and rescue in post-mitotic cells. In proof-of-principle experiments, apterous, a regulator of wing development. was manipulated. Next, conditional null alleles were produced of Glutamic acid decarboxylase 1(Gad1) and Resistant to dieldrin (Rdl), genes vital for GABAergic neurotransmission, as well as cacophony (cac) and paralytic (para), voltage-gated ion channels central to neuronal excitability. To demonstrate the utility of this approach, cac was manipulated in a specific visual interneuron type, and differential regulation of calcium signals was discovered across subcellular compartments. Thus, FlpStop will facilitate investigations into the interactions between genes, circuits, and computation.
Lo, H.G., et al. (2017). A single transcription factor is sufficient to induce and maintain secretory cell architecture. Genes Dev 31: 154-171. PubMed ID: 28174210
Evolutionary Homolog Study:
This study hypothesized that basic helix-loop-helix (bHLH) MIST1 (BHLHA15) (see Drosophila dimm) is a "scaling factor" that universally establishes secretory morphology in cells that perform regulated secretion. That targeted deletion of MIST1 causes dismantling of the secretory apparatus of diverse exocrine cells. Parietal cells (PCs), whose function is to pump acid into the stomach, normally lack MIST1 and do not perform regulated secretion. Forced expression of MIST1 in PCs cause them to expand their apical cytoplasm, rearrange mitochondrial/lysosome trafficking, and generate large secretory granules. Mist1 induces a cohort of genes regulated by MIST1 in multiple organs but does not affect PC function. MIST1 bound CATATG/CAGCTG E boxes in the first intron of genes that regulate autophagosome/lysosomal degradation, mitochondrial trafficking, and amino acid metabolism. Similar alterations in cell architecture and gene expression were also caused by ectopically inducing MIST1 in vivo in hepatocytes. Thus, MIST1 is a scaling factor necessary and sufficient by itself to induce and maintain secretory cell architecture. These results indicate that cells performing similar physiological functions throughout the body share similar transcription factor-mediated architectural "blueprints."

van Tienen, L. M., Mieszczanek, J., Fiedler, M., Rutherford, T. J. and Bienz, M. (2017). Constitutive scaffolding of multiple Wnt enhanceosome components by Legless/BCL9. Elife 6. PubMed ID: 28296634
Wnt/β-catenin signaling elicits context-dependent transcription switches that determine normal development and oncogenesis. These are mediated by the Wnt enhanceosome, a multiprotein complex binding to the Pygo chromatin reader and acting through TCF/LEF-responsive enhancers. Pygo renders this complex Wnt-responsive, by capturing β-catenin via the Legless/BCL9 adaptor. This study used CRISPR/Cas9 genome engineering of Drosophila legless (lgs) and human BCL9 and B9L to show that the C-terminus downstream of their adaptor elements is crucial for Wnt responses. BioID proximity labeling revealed that BCL9 and B9L, like PYGO2, are constitutive components of the Wnt enhanceosome. Wnt-dependent docking of β-catenin to the enhanceosome apparently causes a rearrangement that apposes the BCL9/B9L C-terminus to TCF. This C-terminus binds to the Groucho/TLE co-repressor, and also to the Chip/LDB1-SSDP enhanceosome core complex via an evolutionary conserved element. An unexpected link between BCL9/B9L, PYGO2 and nuclear co-receptor complexes suggests that these β-catenin co-factors may coordinate Wnt and nuclear hormone responses (van Tienen, 2017).
Schor, I. E., Degner, J. F., Harnett, D., Cannavo, E., Casale, F. P., Shim, H., Garfield, D. A., Birney, E., Stephens, M., Stegle, O. and Furlong, E. E. (2017). Promoter shape varies across populations and affects promoter evolution and expression noise. Nat Genet. PubMed ID: 28191888
Animal promoters initiate transcription either at precise positions (narrow promoters) or dispersed regions (broad promoters), a distinction referred to as promoter shape. Although highly conserved, the functional properties of promoters with different shapes and the genetic basis of their evolution remain unclear. This study used natural genetic variation across a panel of 81 Drosophila lines to measure changes in transcriptional start site (TSS) usage, identifying thousands of genetic variants affecting transcript levels (strength) or the distribution of TSSs within a promoter (shape). The results identify promoter shape as a molecular trait that can evolve independently of promoter strength. Broad promoters typically harbor shape-associated variants, with signatures of adaptive selection. Single-cell measurements demonstrate that variants modulating promoter shape often increase expression noise, whereas heteroallelic interactions with other promoter variants alleviate these effects. These results uncover new functional properties of natural promoters and suggest the minimization of expression noise as an important factor in promoter evolution.

Wednesday, March 22nd

Tsuyama, T., Tsubouchi, A., Usui, T., Imamura, H. and Uemura, T. (2017). Mitochondrial dysfunction induces dendritic loss via eIF2α phosphorylation. J Cell Biol 216: 815-834. PubMed ID: 28209644
Mitochondria are key contributors to the etiology of diseases associated with neuromuscular defects or neurodegeneration. How changes in cellular metabolism specifically impact neuronal intracellular processes and cause neuropathological events is still unclear. This study dissects the molecular mechanism by which mitochondrial dysfunction induced by Prel aberrant function mediates selective dendritic loss in Drosophila melanogaster class IV dendritic arborization neurons. Using in vivo ATP imaging, it was found that neuronal cellular ATP levels during development are not correlated with the progression of dendritic loss. By searching for mitochondrial stress signaling pathways that induce dendritic loss it was found that mitochondrial dysfunction is associated with increased eIF2α phosphorylation, which is sufficient to induce dendritic pathology in class IV arborization neurons. It was also observed that eIF2α phosphorylation mediates dendritic loss when mitochondrial dysfunction results from other genetic perturbations. Furthermore, mitochondrial dysfunction induces translation repression in class IV neurons in an eIF2α phosphorylation-dependent manner, suggesting that differential translation attenuation among neuron subtypes is a determinant of preferential vulnerability.

Shukla, J. P., Deshpande, G. and Shashidhara, L. S. (2017). Ataxin-2 binding protein 1 is a context-specific positive regulator of Notch signaling during neurogenesis in Drosophila melanogaster. Development [Epub ahead of print]. PubMed ID: 28174239
The role of Notch pathway during lateral inhibition underlying binary cell fate choice is extensively studied, although context-specificity that generates diverse outcomes is relatively less well understood. In the peripheral nervous system of Drosophila melanogaster, differential Notch signaling between cells of proneural cluster orchestrates sensory organ specification. This study reports functional analysis of Drosophila Ataxin2 binding protein1 (dA2BP1; RNA-binding Fox protein 1) during this process. It's human orthologue A2BP1 is linked to type 2 Spinocerebellar ataxia and other complex neuronal disorders. Downregulation of dA2BP1 in the proneural cluster increases adult sensory bristle number whereas it's over-expression results in loss of bristles. dA2BP1 regulates sensory organ specification by potentiating Notch signaling. Supporting its direct involvement, the biochemical analysis shows that dA2BP1 is part of the Suppressor of Hairless (Su(H)) complex both in the presence and absence of Notch. However, in the absence of Notch signaling, the dA2BP1 interacting fraction of Su(H) does not associate with the repressor proteins, Groucho and CtBP. Based on these data a model is proposed explaining requirement of dA2BP1 as a positive regulator of Notch, whose activity is context-specific.
Song, W., Cheng, D., Hong, S., Sappe, B., Hu, Y., Wei, N., Zhu, C., O'Connor, M. B., Pissios, P. and Perrimon, N. (2017). Midgut-derived Activin regulates glucagon-like action in the fat body and glycemic control. Cell Metab 25(2): 386-399. PubMed ID: 28178568
While high-caloric diet impairs insulin response to cause hyperglycemia, whether and how counter-regulatory hormones are modulated by high-caloric diet is largely unknown. This study found that enhanced response of Drosophila adipokinetic hormone (AKH, the glucagon homolog) in the fat body is essential for hyperglycemia associated with a chronic high-sugar diet. The activin type I receptor Baboon (Babo) autonomously increases AKH signaling without affecting insulin signaling in the fat body via, at least, increase of Akh receptor (AkhR) expression. Further, it was demonstrated that Activin-β (Acβ), an activin ligand predominantly produced in the enteroendocrine cells (EEs) of the midgut, is upregulated by chronic high-sugar diet and signals through Babo to promote AKH action in the fat body, leading to hyperglycemia. Importantly, activin signaling in mouse primary hepatocytes also increases glucagon response and glucagon-induced glucose production, indicating a conserved role for activin in enhancing AKH/glucagon signaling and glycemic control.
Walker, L. J., Summers, D. W., Sasaki, Y., Brace, E. J., Milbrandt, J. and DiAntonio, A. (2017). MAPK signaling promotes axonal degeneration by speeding the turnover of the axonal maintenance factor NMNAT2. Elife 6. PubMed ID: 28095293
Injury-induced (Wallerian) axonal degeneration is regulated via the opposing actions of pro-degenerative factors such as SARM1 and a MAPK signal and pro-survival factors, the most important of which is the NAD+ biosynthetic enzyme NMNAT2 that inhibits activation of the SARM1 pathway. This study investigated the mechanism by which MAPK signaling facilitates axonal degeneration. MAPK signaling was shown to promote the turnover of the axonal survival factor NMNAT2 in cultured mammalian neurons as well as the Drosophila ortholog dNMNAT in motoneurons. The increased levels of NMNAT2 are required for the axonal protection caused by loss of MAPK signaling. Regulation of NMNAT2 by MAPK signaling does not require SARM1, and so cannot be downstream of SARM1. Hence, pro-degenerative MAPK signaling functions upstream of SARM1 by limiting the levels of the essential axonal survival factor NMNAT2 to promote injury-dependent SARM1 activation. These findings are consistent with a linear molecular pathway for the axonal degeneration program.
Rapisarda, V., Borghesan, M., Miguela, V., Encheva, V., Snijders, A. P., Lujambio, A. and O'Loghlen, A. (2017). Integrin β 3 regulates cellular senescence by activating the TGF-β pathway. Cell Rep 18(10): 2480-2493. PubMed ID: 28273461
Evolutionary Homolog Study

Cellular senescence is an important in vivo mechanism that prevents the propagation of damaged cells. However, the precise mechanisms regulating senescence are not well characterized. This study found that ITGB3 (integrin β 3 or β3; see Drosophila Myospheroid) is regulated by the Polycomb protein CBX7. β3 expression accelerates the onset of senescence in human primary fibroblasts by activating the transforming growth factor β (TGF-β) pathway in a cell-autonomous and non-cell-autonomous manner. β3 levels are dynamically increased during oncogene-induced senescence (OIS) through CBX7 Polycomb regulation, and downregulation of β3 levels overrides OIS and therapy-induced senescence (TIS), independently of its ligand-binding activity. Moreover, cilengitide, an αvβ3 antagonist, has the ability to block the senescence-associated secretory phenotype (SASP) without affecting proliferation. Finally, this study shows an increase in β3 levels in a subset of tissues during aging. Altogether, these data show that integrin β3 subunit is a marker and regulator of senescence.

Chakraborty, S., Njah, K., Pobbati, A. V., Lim, Y. B., Raju, A., Lakshmanan, M., Tergaonkar, V., Lim, C. T. and Hong, W. (2017). Agrin as a Mechanotransduction Signal Regulating YAP through the Hippo Pathway. Cell Rep 18(10): 2464-2479. PubMed ID: 28273460
Evolutionary Homolog Study
The Hippo pathway effectors YAP and TAZ (see Drosophila Yorkie) act as nuclear sensors of mechanical signals in response to extracellular matrix (ECM) cues. However, the identity and nature of regulators in the ECM and the precise pathways relaying mechanoresponsive signals into intracellular sensors remain unclear. This study uncovered a functional link between the ECM proteoglycan Agrin and the transcriptional co-activator YAP. Importantly, Agrin transduces matrix and cellular rigidity signals that enhance stability and mechanoactivity of YAP through the integrin-focal adhesion- and Lrp4/MuSK receptor-mediated signaling pathways. Agrin antagonizes focal adhesion assembly of the core Hippo components by facilitating ILK-PAK1 (see Drosophila Pak) signaling and negating the functions of Merlin and LATS1/2 (see Drosophila Merlin and Warts). It was further shown that Agrin promotes oncogenesis through YAP-dependent transcription and is clinically relevant in human liver cancer. It is proposed that Agrin acts as a mechanotransduction signal in the ECM.

Tuesday, March 21st

Gerland, T.A., Sun, B., Smialowski, P., Lukacs, A., Thomae, A.W. and Imhof, A. (2017). The Drosophila speciation factor HMR localizes to genomic insulator sites. PLoS One 12: e0171798. PubMed ID: 28207793
Hybrid incompatibility between Drosophila melanogaster and D. simulans is caused by a lethal interaction of the proteins encoded by the Hmr (Hybrid male rescue) and Lhr (Lethal hybrid rescue) genes. In D. melanogaster the loss of HMR results in mitotic defects, an increase in transcription of transposable elements and a deregulation of heterochromatic genes. To better understand the molecular mechanisms that mediate HMR's function, this study measured genome-wide localization of HMR in D. melanogaster tissue culture cells by chromatin immunoprecipitation. Interestingly, HMR was found to localize to genomic insulator sites that can be classified into two groups. One group belongs to gypsy insulators and another one borders HP1a bound regions at active genes. The transcription of the latter group genes is strongly affected in larvae and ovaries of Hmr mutant flies. These data suggest a novel link between HMR and insulator proteins, a finding that implicates a potential role for genome organization in the formation of species.

Amendola, P.G., Zaghet, N., Ramalho, J.J., Vilstrup Johansen, J., Boxem, M. and Salcini, A.E. (2017). JMJD-5/KDM8 regulates H3K36me2 and is required for late steps of homologous recombination and genome integrity. PLoS Genet 13: e1006632. PubMed ID: 28207814
Evolutionary Homolog Study:
Methylation of lysine 36 of histone 3 (H3K36) is a post-translational modification functionally relevant during early steps of DNA damage repair (see Drosophila DNA damage repair). This study shows that the JMJD-5 (see Drosophila CG13902) regulates H3K36 di-methylation and is required at late stages of double strand break repair mediated by homologous recombination. Loss of jmjd-5 results in hypersensitivity to ionizing radiation and meiotic defects, and it is associated with aberrant retention of RAD-51 (see Drosophila spn-A) at sites of double strand breaks. Analyses o jmjd-5 genetic interactions with genes required for resolving recombination intermediates (rtel-1 (see Drosophila CG4078)) or promoting the resolution of RAD-51 double stranded DNA filaments (rfs-1 and helq-1 (see Drosophila mus301)) suggest that jmjd-5 prevents the formation of stalled postsynaptic recombination intermediates and favors RAD-51 removal. As these phenotypes are all recapitulated by a catalytically inactive jmjd-5 mutant, the study proposes a novel role for H3K36me2 regulation during late steps of homologous recombination critical to preserve genome integrity.

Huang, C., Su, T., Xue, Y., Cheng, C., Lay, F.D., McKee, R.A., Li, M., Vashisht, A., Wohlschlegel, J., Novitch, B.G., Plath, K., Kurdistani, S.K. and Carey, M. (2017). Cbx3 maintains lineage specificity during neural differentiation. Genes Dev 31: 241-246. PubMed ID: 28270516
Evolutionary Homology Study:
Chromobox homolog 3 (Cbx3/heterochromatin protein 1γ [HP1γ]) (see Drosophila HP1b) stimulates cell differentiation, but its mechanism is unknown. This study found that Cbx3 binds to gene promoters upon differentiation of murine embryonic stem cells (ESCs) to neural progenitor cells (NPCs) and recruits the Mediator subunit Med26 (see Drosophila MED26). RNAi knockdown of either Cbx3 or Med26 inhibits neural differentiation while up-regulating genes involved in mesodermal lineage decisions. Thus, Cbx3 and Med26 together ensure the fidelity of lineage specification by enhancing the expression of neural genes and down-regulating genes specific to alternative fates.

Laprell, F., Finkl, K. and Muller, J. (2017). Propagation of Polycomb-repressed chromatin requires sequence-specific recruitment to DNA. Science [Epub ahead of print]. PubMed ID: 28302792
Epigenetic inheritance models posit that during Polycomb repression, Polycomb Repressive Complex 2 (PRC2) propagates histone H3K27 tri-methylation (H3K27me3) independently of DNA sequence. This study shows that insertion of Polycomb Response Element (PRE) DNA into the Drosophila genome creates extended domains of H3K27me3-modified nucleosomes in the flanking chromatin and causes repression of a linked reporter gene. After excision of PRE DNA, H3K27me3 nucleosomes become diluted with each round of DNA replication and reporter gene repression is lost, whereas in replication-stalled cells, H3K27me3 levels stay high and repression persists. Hence, H3K27me3-marked nucleosomes provide a memory of repression that is transmitted in a sequence-independent manner to daughter strand DNA during replication. In contrast, propagation of H3K27 tri-methylation to newly incorporated nucleosomes requires sequence-specific targeting of PRC2 to PRE DNA.

Monday, March 20th

Newman, Z. L., Hoagland, A., Aghi, K., Worden, K., Levy, S. L., Son, J. H., Lee, L. P. and Isacoff, E. Y. (2017). Input-specific plasticity and homeostasis at the Drosophila larval neuromuscular junction. Neuron. PubMed ID: 28285823
Synaptic connections undergo activity-dependent plasticity during development and learning, as well as homeostatic re-adjustment to ensure stability. Little is known about the relationship between these processes, particularly in vivo. This was addressed with novel quantal resolution imaging of transmission during locomotive behavior at glutamatergic synapses of the Drosophila larval neuromuscular junction. Two motor input types, Ib and Is, were found to provide distinct forms of excitatory drive during crawling and differ in key transmission properties. Although both inputs vary in transmission probability, active Is synapses are more reliable. High-frequency firing 'wakes up' silent Ib synapses and depresses Is synapses. Strikingly, homeostatic compensation in presynaptic strength only occurs at Ib synapses. This specialization is associated with distinct regulation of postsynaptic CaMKII. Thus, basal synaptic strength, short-term plasticity, and homeostasis are determined input-specifically, generating a functional diversity that sculpts excitatory transmission and behavioral function (Newman, 2017).
Dey, S., Banker, G. and Ray, K. (2017). Anterograde Transport of Rab4-Associated Vesicles Regulates Synapse Organization in Drosophila. Cell Rep 18(10): 2452-2463. PubMed ID: 28273459
Local endosomal recycling at synapses is essential to maintain neurotransmission. Rab4 GTPase, found on sorting endosomes, is proposed to balance the flow of vesicles among endocytic, recycling, and degradative pathways in the presynaptic compartment. This study reports that Rab4-associated vesicles move bidirectionally in Drosophila axons but with an anterograde bias, resulting in their moderate enrichment at the synaptic region of the larval ventral ganglion. Results from FK506 binding protein (FKBP) and FKBP-Rapamycin binding domain (FRB) conjugation assays in rat embryonic fibroblasts together with genetic analyses in Drosophila indicate that an association with Kinesin-2 (mediated by the tail domain of Kinesin-2α/KIF3A/KLP64D subunit) moves Rab4-associated vesicles toward the synapse. Reduction in the anterograde traffic of Rab4 causes an expansion of the volume of the synapse-bearing region in the ventral ganglion and increases the motility of Drosophila larvae. These results suggest that Rab4-dependent vesicular traffic toward the synapse plays a vital role in maintaining synaptic balance in this neuronal network.
McNally, E.K., Karim, M.A. and Brett, C.L. (2017). Selective lysosomal transporter degradation by organelle membrane fusion. Dev Cell 40: 151-167. PubMed ID: 28017618
Evolutionary Homology Study:
Lysosomes (see Drosophila vesicles) rely on their resident transporter proteins to return products of catabolism to the cell for reuse and for cellular signaling, metal storage, and maintaining the lumenal environment. Despite their importance, little is known about the lifetime of these transporters or how they are regulated. Using Saccharomyces cerevisiae as a model, this study discovered a new pathway intrinsic to homotypic lysosome membrane fusion that is responsible for their degradation. Transporter proteins are selectively sorted by the docking machinery into an area between apposing lysosome membranes, which is internalized and degraded by lumenal hydrolases upon organelle fusion. These proteins have diverse lifetimes that are regulated in response to protein misfolding, changing substrate levels, or TOR (see Drosophila TOR) activation. Analogous to endocytosis for controlling surface protein levels, the "intralumenal fragment pathway" is critical for lysosome membrane remodeling required for organelle function in the context of cellular protein quality control, ion homeostasis, and metabolism.
Yeun Lee, J., Geng, J., Lee, J., Wang, A.R. and Chang, K.T. (2017). Activity-induced synaptic structural modifications by an activator of integrin signaling at the Drosophila neuromuscular junction. J Neurosci [Epub ahead of print]. PubMed ID: 28219985
Activity-induced synaptic structural modification is crucial for neural development and synaptic plasticity, but the molecular players involved in this process are not well defined. This study reports that a protein named Shriveled, Shv, regulates synaptic growth and activity-dependent synaptic remodeling at the Drosophila neuromuscular junction. Depletion of Shv causes synaptic overgrowth and an accumulation of immature boutons. Shv physically and genetically interacts with βPS integrin. Furthermore, Shv is secreted during intense, but not mild, neuronal activity to acutely activate integrin signaling, induce synaptic bouton enlargement, and increase postsynaptic glutamate receptor abundance. Consequently, loss of Shv prevents activity-induced synapse maturation and abolishes post-tetanic potentiation, a form of synaptic plasticity. These data identify Shv as a novel trans-synaptic signal secreted upon intense neuronal activity to promote synapse remodeling through integrin receptor signaling

Sunday, March 19th

Teesalu, M., Rovenko, B. M. and Hietakangas, V. (2017). Salt-Inducible kinase 3 provides sugar tolerance by regulating NADPH/NADP+ redox balance. Curr Biol 27(3): 458-464. PubMed ID: 28132818
Nutrient-sensing pathways respond to changes in the levels of macronutrients, such as sugars, lipids, or amino acids, and regulate metabolic pathways to maintain organismal homeostasis. Consequently, nutrient sensing provides animals with the metabolic flexibility necessary for enduring temporal fluctuations in nutrient intake. Recent studies have shown that an animal's ability to survive on a high-sugar diet is determined by sugar-responsive gene regulation. It remains to be elucidated whether other levels of metabolic control, such as post-translational regulation of metabolic enzymes, also contribute to organismal sugar tolerance. Furthermore, the sugar-regulated metabolic pathways contributing to sugar tolerance remain insufficiently characterized. This study identified Salt-inducible kinase 3 (SIK3), a member of the AMP-activated protein kinase (AMPK)-related kinase family, as a key determinant of Drosophila sugar tolerance. SIK3 allows sugar-feeding animals to increase the reductive capacity of nicotinamide adenine dinucleotide phosphate (NADPH/NADP+). NADPH mediates the reduction of the intracellular antioxidant glutathione, which is essential for survival on a high-sugar diet. SIK3 controls NADP+ reduction by phosphorylating and activating Glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme of the pentose phosphate pathway. SIK3 gene expression is regulated by the sugar-regulated transcription factor complex Mondo-Mlx, which was previously identified as a key determinant of sugar tolerance. SIK3 converges with Mondo-Mlx in sugar-induced activation of G6PD, and simultaneous inhibition of SIK3 and Mondo-Mlx leads to strong synergistic lethality on a sugar-containing diet. In conclusion, SIK3 cooperates with Mondo-Mlx to maintain organismal sugar tolerance through the regulation of NADPH/NADP+ redox balance.
Mossman, J. A., Tross, J. G., Jourjine, N. A., Li, N., Wu, Z. and Rand, D. M. (2016). Mitonuclear interactions mediate transcriptional responses to hypoxia in Drosophila. Mol Biol Evol [Epub ahead of print]. PubMed ID: 28110272
Among the major challenges in quantitative genetics and personalized medicine is to understand how gene x gene interactions (G x G: epistasis) and gene x environment interactions (G x E) underlie phenotypic variation. This study used the intimate relationship between mitochondria and oxygen availability to dissect the roles of nuclear DNA (nDNA) variation, mitochondrial DNA (mtDNA) variation, hypoxia, and their interactions on gene expression in Drosophila melanogaster. Mitochondria provide an important evolutionary and medical context for understanding G x G and G x E given their central role in integrating cellular signals. It was hypothesized that hypoxia would alter mitonuclear communication and gene expression patterns. First order nDNA, mtDNA, and hypoxia effects were shown to vary between the sexes, along with mitonuclear epistasis and G x G x E effects. Females were generally more sensitive to genetic and environmental perturbation. While dozens to hundreds of genes are altered by hypoxia in individual genotypes, very little overlap was found among mitonuclear genotypes for genes that were significantly differentially expressed as a consequence of hypoxia; excluding the gene hairy. Oxidative phosphorylation genes were among the most influenced by hypoxia and mtDNA, and exposure to hypoxia increased the signature of mtDNA effects, suggesting retrograde signaling between mtDNA and nDNA. nDNA-encoded genes were identified in the electron transport chain (succinate dehydrogenase) that exhibit female-specific mtDNA effects. These findings have important implications for personalized medicine, the sex-specific nature of mitonuclear communication, and gene x gene coevolution under variable or changing environments.
Salminen, T.S., Oliveira, M.T., Cannino, G., Lillsunde, P., Jacobs, H.T. and Kaguni, L.S. (2017). Mitochondrial genotype modulates mtDNA copy number and organismal phenotype in Drosophila. Mitochondrion [Epub ahead of print]. PubMed ID: 28214560
This study evaluated the role of natural mitochondrial DNA (mtDNA) variation on mtDNA copy number, biochemical features and life history traits in Drosophila hybrid strains. The effects of both coding region and non-coding A+T region variation on mtDNA copy number were demonstrated. It was also found that copy number correlates with mitochondrial biochemistry and metabolically important traits such as development time. For example, high mtDNA copy number correlates with longer development times. These findings support the hypothesis that mtDNA copy number is modulated by mtDNA genome variation and suggest that it affects OXPHOS efficiency through changes in the organization of the respiratory membrane complexes to influence organismal phenotype.

Le Manh, H., Guio, L., Merenciano, M., Rovira, Q., Barrón, M.G. and González, J. (2017). Natural and laboratory mutations in kuzbanian are associated with zinc stress phenotypes in Drosophila melanogaster. Sci Rep 7: 42663. PubMed ID: 28218276
Stress response to heavy metals is mediated by the metal-responsive transcription factor 1 (MTF-1). MTF-1 binds to metal response elements (MREs) and changes the expression of target genes. kuzbanian (kuz), a metalloendopeptidase that activates the evolutionary conserved Notch signaling pathway, has been identified as an MTF-1 target gene. FBti0019170, inserted in a kuz intron, is putatively adaptive transposable element in the Drosophila genome. This study investigated whether a laboratory mutant stock overexpressing kuz is associated with zinc stress phenotypes. It was found that both embryos and adult flies overexpressing kuz are more tolerant to zinc compared with wild-type flies. On the other hand, the effect of FBti0019170 on zinc stress tolerance depends on developmental stage and genetic background. In the majority of the genetic backgrounds analyzed, FBti0019170 has a deleterious effect in unpolluted environments in pre-adult stages.

Saturday, March 18th

Pegoraro, M., Zonato, V., Tyler, E. R., Fedele, G., Kyriacou, C. P. and Tauber, E. (2017). Geographical analysis of diapause inducibility in European Drosophila melanogaster populations. J Insect Physiol 98: 238-244. PubMed ID: 28131702
Seasonal overwintering in insects represents an adaptation to stressful environments and in European Drosophila melanogaster females, low temperatures and short photoperiods can induce an ovarian diapause. Diapause may represent a recent (<15Ky) adaptation to the colonisation of temperate Europe by D. melanogaster from tropical sub-Saharan Africa, because African D. melanogaster and the sibling species D. simulans, have been reported to fail to undergo diapause. Over the past few centuries, D. melanogaster have also invaded North America and Australia, and eastern populations on both continents show a predictable latitudinal cline in diapause induction. In Europe however, a new diapause-enhancing timeless allele, ls-tim, is observed at high levels in southern Italy ( approximately 80%), where it appears to have arisen and has spread throughout the continent with a frequency of approximately 20% in Scandinavia. Given the phenotype of ls-tim and its geographical distribution, it was predicted that it would work against any latitudinal cline in diapause induction within Europe. Indeed this study revealed that any latitudinal cline for diapause in Europe is very weak, as predicted by ls-tim frequencies. In contrast, ls-tim frequencies were determined in North America and it was observed that they would be expected to strengthen the latitudinal pattern of diapause. The results reveal how a newly arisen mutation, can, via the stochastic nature of where it initially arose, blur an otherwise adaptive geographical pattern.
Shindey, R., Varma, V., Nikhil, K. L. and Sharma, V. K. (2017). Evolution of circadian rhythms in Drosophila melanogaster populations reared in constant light and dark regimes for over 330 generations. Chronobiol Int: 1-14. PubMed ID: 28156168
Organisms are believed to have evolved circadian clocks as adaptations to deal with cyclic environmental changes, and therefore it has been hypothesized that evolution in constant environments would lead to regression of such clocks. This study examined whether circadian clocks and the associated properties evolve differently under constant light and constant darkness. Activity-rest, adult emergence and oviposition rhythms were measured of D. melanogaster populations that have been maintained for over 19 years (~330 generations) under three different light regimes - constant light (LL), light-dark cycles of 12:12 h (LD) and constant darkness (DD). While circadian rhythms in all the three behaviors persist in both LL and DD stocks with no differences in circadian period, they differed in certain aspects of the entrained rhythms when compared to controls reared in rhythmic environment (LD). Interestingly, it was also observed that DD stocks have evolved significantly higher robustness or power of free-running activity-rest and adult emergence rhythms compared to LL stocks. Thus, this study, in addition to corroborating previous results of circadian clock evolution in constant light, also highlights that, contrary to the expected regression of circadian clocks, rearing in constant darkness leads to the evolution of more robust circadian clocks which may be attributed to an intrinsic adaptive advantage of circadian clocks and/or pleiotropic functions of clock genes in other traits.
Prieto-Godino, L. L., Rytz, R., Cruchet, S., Bargeton, B., Abuin, L., Silbering, A. F., Ruta, V., Dal Peraro, M. and Benton, R. (2017). Evolution of acid-sensing olfactory circuits in Drosophilids. Neuron 93(3): 661-676.e666. PubMed ID: 28111079
Animals adapt their behaviors to specific ecological niches, but the genetic and cellular basis of nervous system evolution is poorly understood. This study compared the olfactory circuits of the specialist Drosophila sechellia-which feeds exclusively on Morinda citrifolia fruit-with its generalist cousins D. melanogaster and D. simulans. D. sechellia was shown to exhibit derived odor-evoked attraction and physiological sensitivity to the abundant Morinda volatile hexanoic acid, and how the responsible sensory receptor (the variant ionotropic glutamate receptor IR75b) and attraction-mediating circuit have evolved were characterized. A single amino acid change in IR75b is sufficient to recode it as a hexanoic acid detector. Expanded representation of this sensory pathway in the brain relies on additional changes in the IR75b promoter and trans-acting loci. By contrast, higher-order circuit adaptations are not apparent, suggesting conserved central processing. This work links olfactory ecology to structural and regulatory genetic changes influencing nervous system anatomy and function.
Mittleman, B. E., Manzano-Winkler, B., Hall, J. B., Korunes, K. L. and Noor, M. A. (2017). The large X-effect on secondary sexual characters and the genetics of variation in sex comb tooth number in Drosophila subobscura. Ecol Evol 7(2): 533-540. PubMed ID: 28116050
This study examined the genetics of a secondary sexual trait, male sex comb size in Drosophila subobscura, to evaluate the amount of variation attributable to the X-chromosome. This species bears unusually large sex combs for its species group, and therefore, this trait may be a good candidate for having been affected by natural or sexual selection. Significant heritable variation was observed in number of teeth of the distal sex comb across strains. While reciprocal F1 crosses seemed to implicate a disproportionate X-chromosome effect, further examination in the F2 progeny showed that transgressive autosomal effects inflated the estimate of variation associated with the X-chromosome in the F1. Instead, the X-chromosome appears to confer the smallest contribution of all major chromosomes to the observed phenotypic variation. Further, effects on copulation latency or duration associated with the observed phenotypic variation were not observed. Overall, this study presents an examination of the genetics underlying segregating phenotypic variation within species and illustrates two common pitfalls associated with some past studies of the genetic basis of secondary sexual traits.

Friday, March 17th

]Park, S.M., Park, H.R. and Lee, J.H. (2017). MAPK3 at the autism-linked human 16p11.2 locus influences precise synaptic target selection at Drosophila larval neuromuscular junctions. Mol Cells [Epub ahead of print]. PubMed ID: 28196412
Proper synaptic function in neural circuits requires precise pairings between correct pre- and post-synaptic partners. Errors in this process may underlie development of neuropsychiatric disorders, such as autism spectrum disorder (ASD). Development of ASD can be influenced by genetic factors, including copy number variations (CNVs). This study focused on a CNV occurring at the 16p11.2 locus in the human genome and investigated potential defects in synaptic connectivity caused by reduced activities of genes located in this region at Drosophila larval neuromuscular junctions, a well-established model synapse with stereotypic synaptic structures. A mutation of rolled, the Drosophila homolog of human mitogen-activated protein kinase 3 (MAPK3) at the 16p11.2 locus, causes ectopic innervation of axonal branches and their abnormal defasciculation. The specificity of these phenotypes was confirmed by expression of wild-type rolled in the mutant background. Albeit to a lesser extent, ectopic innervation patterns were also observed in mutants defective in Cdk2, Gaq, and Gp93, all of which are expected to interact with Rolled MAPK3. Further genetic analysis in double heterozygous combinations reveals a synergistic interaction between rolled and Gp93. In addition, results from RT-qPCR analyses indicate consistently reduced rolled mRNA levels in Cdk2, Gaq, and Gp93 mutants. Taken together, these data suggest a central role of MAPK3 in regulating the precise targeting of presynaptic axons to proper postsynaptic targets, a critical step that may be altered significantly in ASD.

Pascua-Maestro, R., Diez-Hermano, S., Lillo, C., Ganfornina, M. D. and Sanchez, D. (2017). Protecting cells by protecting their vulnerable lysosomes: Identification of a new mechanism for preserving lysosomal functional integrity upon oxidative stress. PLoS Genet 13(2): e1006603. PubMed ID: 28182653
Environmental insults such as oxidative stress can damage cell membranes. Lysosomes are particularly sensitive to membrane permeabilization since their function depends on intraluminal acidic pH and requires stable membrane-dependent proton gradients. Lipocalin Apolipoprotein D (ApoD) is an extracellular lipid binding protein endowed with antioxidant capacity. This study performed a comprehensive analysis of ApoD intracellular traffic and demonstrates its role in lysosomal pH homeostasis upon paraquat-induced oxidative stress. ApoD was shown to be endocytosed and targeted to a subset of vulnerable lysosomes in a stress-dependent manner. ApoD is functionally stable in this acidic environment, and its presence is sufficient and necessary for lysosomes to recover from oxidation-induced alkalinization, both in astrocytes and neurons. This function is accomplished by preventing lysosomal membrane permeabilization. Two lysosomal-dependent biological processes, myelin phagocytosis by astrocytes and optimization of neurodegeneration-triggered autophagy in a Drosophila in vivo model, require ApoD-related Lipocalins (see Glial Lazarillo). These results set a lipoprotein-mediated regulation of lysosomal membrane integrity as a new mechanism at the hub of many cellular functions, critical for the outcome of a wide variety of neurodegenerative diseases.
Perry, S., Kiragasi, B., Dickman, D. and Ray, A. (2017). The role of Histone Deacetylase 6 in synaptic plasticity and memory. Cell Rep 18: 1337-1345. PubMed ID: 28178513
Histone deacetylases (HDACs) have been extensively studied as drug targets in neurodegenerative diseases, but less is known about their role in healthy neurons. This study tested zinc-dependent HDACs using RNAi in Drosophila melanogaster and found memory deficits with RPD3 and HDAC6. HDAC6 was found to be required in both the larval and adult stages for normal olfactory memory retention. Neuronal expression of HDAC6 rescues memory deficits, and the N-terminal deacetylase (DAC) domain is required for this ability. This suggests that deacetylation of synaptic targets associated with the first DAC domain, such as the active-zone scaffold Bruchpilot, is required for memory retention. Finally, electrophysiological experiments at the neuromuscular junction reveal that HDAC6 mutants exhibit a partial block of homeostatic plasticity, suggesting that HDAC6 may be required for the stabilization of synaptic strength. The learning deficit observed in HDAC6 mutants could be a behavioral consequence of these synaptic defects.

Vonk, J. J., et al. (2017). Drosophila Vps13 Is required for protein homeostasis in the brain. PLoS One 12(1): e0170106. PubMed ID: 28107480
Chorea-Acanthocytosis is a rare, neurodegenerative disorder characterized by progressive loss of locomotor and cognitive function. It is caused by loss of function mutations in the Vacuolar Protein Sorting 13A (VPS13A) gene. This study characterized a Drosophila Vps13 mutant line. The data suggest that Vps13 is a peripheral membrane protein located to endosomal membranes and enriched in the fly head. Vps13 mutant flies showed a shortened life span and age associated neurodegeneration. Vps13 mutant flies were sensitive to proteotoxic stress and accumulated ubiquitylated proteins. Levels of Ref(2)P, the Drosophila orthologue of p62, were increased and protein aggregates accumulated in the central nervous system. Overexpression of the human Vps13A protein in the mutant flies partly rescued apparent phenotypes. This suggests a functional conservation of human VPS13A and Drosophila Vps13. The results demonstrate that Vps13 is essential to maintain protein homeostasis in the larval and adult Drosophila brain. Drosophila Vps13 mutants are suitable to investigate the function of Vps13 in the brain, to identify genetic enhancers and suppressors and to screen for potential therapeutic targets for Chorea-Acanthocytosis.

Thursday, March 16

Sechi, S., Frappaolo, A., Fraschini, R., Capalbo, L., Gottardo, M., Belloni, G., Glover, D. M., Wainman, A. and Giansanti, M. G. (2017). Rab1 interacts with GOLPH3 and controls Golgi structure and contractile ring constriction during cytokinesis in Drosophila melanogaster. Open Biol 7(1). PubMed ID: 28100664
Cytokinesis requires a tight coordination between actomyosin ring constriction and new membrane addition along the ingressing cleavage furrow. However, the molecular mechanisms underlying vesicle trafficking to the equatorial site and how this process is coupled with the dynamics of the contractile apparatus are poorly defined. This study provides evidence for the requirement of Rab1 during cleavage furrow ingression in cytokinesis. The gene omelette (omt) was found encodes the Drosophila orthologue of human Rab1 and is required for successful cytokinesis in both mitotic and meiotic dividing cells of Drosophila melanogaster. Rab1 protein colocalizes with the conserved oligomeric Golgi (COG) complex Cog7 subunit and the phosphatidylinositol 4-phosphate effector GOLPH3 at the Golgi stacks. Analysis by transmission electron microscopy and 3D-SIM super-resolution microscopy reveals loss of normal Golgi architecture in omt mutant spermatocytes indicating a role for Rab1 in Golgi formation. In dividing cells, Rab1 enables stabilization and contraction of actomyosin rings. It was further demonstrated that GTP-bound Rab1 directly interacts with GOLPH3 and controls its localization at the Golgi and at the cleavage site. It is proposed that Rab1, by associating with GOLPH3, controls membrane trafficking and contractile ring constriction during cytokinesis.
Duda, H., Arter, M., Gloggnitzer, J., Teloni, F., Wild, P., Blanco, M.G., Altmeyer, M. and Matos, J. (2016). A mechanism for controlled breakage of under-replicated chromosomes during mitosis. Dev Cell 39: 740-755. PubMed ID: 27997828
Evolutionary Homolog Study:
While DNA replication and mitosis occur in a sequential manner, precisely how cells maintain their temporal separation and order remains elusive. This study unveils a double-negative feedback loop between replication intermediates and an M-phase-specific structure-selective endonuclease, MUS81-SLX4 (see Drosophila Mus81 and Mus312), which renders DNA replication and mitosis mutually exclusive. MUS81 nuclease is constitutively active throughout the cell cycle (see Drosophila cell cycle) but requires association with SLX4 for efficient substrate targeting. To preclude toxic processing of replicating chromosomes, WEE1 (see Drosophila Wee1) kinase restrains CDK1 (see Drosophila Cdk1) and PLK1 (see Drosophila polo)-mediated MUS81-SLX4 assembly during S phase. Accordingly, WEE1 inhibition triggers widespread nucleolytic breakage of replication intermediates, halting DNA replication and leading to chromosome pulverization. Unexpectedly, premature entry into mitosis-licensed by unrestrained CDK1 activity during S phase-requires MUS81-SLX4, which inhibits DNA replication. This suggests that ongoing replication assists WEE1 in delaying entry into M phase and, indirectly, in preventing MUS81-SLX4 assembly. Conversely, MUS81-SLX4 activation during mitosis promotes targeted resolution of persistent replication intermediates, which safeguards chromosome segregation.

Argüello-Miranda, O., Zagoriy, I., Mengoli, V., Rojas, J., Jonak, K., Oz, T., Graf, P. and Zachariae, W. (2017). Casein Kinase 1 coordinates Cohesin cleavage, gametogenesis, and exit from M Phase in Meiosis II. Dev Cell 40: 37-52. PubMed ID: 28017619
Evolutionary Homolog Study:
Meiosis consists of DNA replication followed by two consecutive nuclear divisions and gametogenesis or spore formation. While meiosis I has been studied extensively, less is known about the regulation of meiosis II (see Drosophila cell cycle). This study shows that Hrr25 (see Drosophila dco), the conserved casein kinase 1δ of budding yeast, links three mutually independent key processes of meiosis II. First, Hrr25 induces nuclear division by priming centromeric cohesin for cleavage by separase. Hrr25 simultaneously phosphorylates Rec8 (see Drosophila vtd), the cleavable subunit of cohesin, and removes from centromeres the cohesin protector composed of shugoshin and the phosphatase PP2A. Second, Hrr25 initiates the sporulation program by inducing the synthesis of membranes that engulf the emerging nuclei at anaphase II. Third, Hrr25 mediates exit from meiosis II by activating pathways that trigger the destruction of M-phase-promoting kinases. Thus, Hrr25 synchronizes formation of the single-copy genome with gamete differentiation and termination of meiosis.

McKinley, K. L. and Cheeseman, I. M. (2017). Large-Scale Analysis of CRISPR/Cas9 Cell-Cycle Knockouts Reveals the Diversity of p53-Dependent Responses to Cell-Cycle Defects. Dev Cel 40(4):405-420l. PubMed ID: 28216383
Evolutionary Homolog Study
Defining the genes that are essential for cellular proliferation is critical for understanding organismal development and identifying high-value targets for disease therapies. However, the requirements for cell-cycle progression in human cells remain incompletely understood. To elucidate the consequences of acute and chronic elimination of cell-cycle proteins, this study generated and characterized inducible CRISPR/Cas9 knockout human cell lines targeting 209 genes involved in diverse cell-cycle processes. Single-cell microscopic analyses were performed to systematically establish the effects of the knockouts on subcellular architecture. To define variations in cell-cycle requirements between cultured cell lines, knockouts were generated across cell lines of diverse origins. p53 (see Drosophila p53) was shown to modulate the phenotype of specific cell-cycle defects through distinct mechanisms, depending on the defect. This work provides a resource to broadly facilitate robust and long-term depletion of cell-cycle proteins and reveals insights into the requirements for cell-cycle progression.
Puah, W. C., Chinta, R. and Wasser, M. (2017). Quantitative microscopy uncovers ploidy changes during mitosis in live Drosophila embryos and their effect on nuclear size. Biol Open [Epub ahead of print]. PubMed ID: 28108477
Time-lapse microscopy is a powerful tool to investigate cellular and developmental dynamics. In Drosophila melanogaster, it can be used to study division cycles in embryogenesis. Image analysis of maternal-haploid (mh) embryos revealed that a fraction of haploid syncytial nuclei fused to give rise to nuclei of higher ploidy (2n, 3n, 4n). Moreover, nuclear densities in mh embryos at the mid-blastula transition varied over threefold. By tracking synchronized nuclei of different karyotypes side-by-side, DNA content was shown to determine nuclear growth rate and size in early, while the nuclear to cytoplasmic ratio constrains nuclear growth during late interphase. mh encodes the Drosophila ortholog of human Spartan, a protein involved in DNA damage tolerance. To explore the link between mh and chromosome instability, Mh protein was fluorescently tagged to study its subcellular localization. Mh-mKO2 was shown to localize to nuclear speckles that increase in numbers as nuclei expand in interphase. In summary, quantitative microscopy can provide new insights into well-studied genes and biological processes.
Dorogova, N. V., Bolobolova, E. U. and Zakharenko, L. P. (2017). Cellular aspects of gonadal atrophy in Drosophila P-M hybrid dysgenesis. Dev Biol [Epub ahead of print]. PubMed ID: 28283407
Gonadal atrophy is the most typical and dramatic manifestation of intraspecific hybrid dysgenesis syndrome leading to sterility in Drosophila melanogaster dysgenic progeny. The P-M system of hybrid dysgenesis is primarily associated with germ cell degeneration during the early stages of Drosophila embryonic development at elevated temperatures. This study has have defined the phase of germ cell death as beginning at the end of embryogenesis immediately following gonad formation. However, the temperature-dependent screening of germ cell developmental patterns in the dysgenic background showed that early germ cells are susceptible to the hybrid dysgenesis at any Drosophila life-cycle stage, including in the imago. Electron microscopy of germ cells after dysgenesis induction revealed significant changes in subcellular structure, especially mitochondria, prior to cellular breakdown. The mitochondrial pathology can promote the activation of cell death pathways in dysgenic germ cells, which leads to gonadal atrophy.

Wednesday, March 15th

Muijres, F. T., Iwasaki, N. A., Elzinga, M. J., Melis, J. M. and Dickinson, M. H. (2017). Flies compensate for unilateral wing damage through modular adjustments of wing and body kinematics. Interface Focus 7(1): 20160103. PubMed ID: 28163885
Using high-speed videography, this study investigated how fruit flies compensate for unilateral wing damage, in which loss of area on one wing compromises both weight support and roll torque equilibrium. The results show that flies control for unilateral damage by rolling their body towards the damaged wing and by adjusting the kinematics of both the intact and damaged wings. To compensate for the reduction in vertical lift force due to damage, flies elevate wingbeat frequency. Because this rise in frequency increases the flapping velocity of both wings, it has the undesired consequence of further increasing roll torque. To compensate for this effect, flies increase the stroke amplitude and advance the timing of pronation and supination of the damaged wing, while making the opposite adjustments on the intact wing. The resulting increase in force on the damaged wing and decrease in force on the intact wing function to maintain zero net roll torque. However, the bilaterally asymmetrical pattern of wing motion generates a finite lateral force, which flies balance by maintaining a constant body roll angle. Based on these results and additional experiments using a dynamically scaled robotic fly, a simple bioinspired control algorithm is proposed for asymmetric wing damage.
Nguyen, T. T. and Moehring, A. J. (2017). Cross-generational comparison of reproductive success in recently caught strains of Drosophila melanogaster. BMC Evol Biol 17(1): 41. PubMed ID: 28166714
Males and females often have opposing strategies for increasing reproductive fitness. Males that out-compete others higher lifetime reproductive success. Females that mate with a high quality male receive either direct benefits through productivity or acquisition of additional resources. These components may be in conflict: factors that increase offspring fitness may decrease a female's productivity, and alleles that are beneficial in one sex may be detrimental in the opposite sex. This study used a multigenerational study with recently caught strains of Drosophila melanogaster to examine the relationship between parental, male offspring, and female offspring fitness when fitness is measured in a basal non-competitive environment. Synergy was found between parental and offspring lifetime reproductive success, indicating a lack of parent-offspring conflict, and a synergy was found between son and daughter reproductive success, indicating a lack of intersexual conflict. Interestingly, inbreeding significantly reduced the lifetime reproductive success of daughters, but did not have a significant effect on short-term productivity measures of daughters, sons or parents. It is concluded that in wild-caught flies, there appears to be no parent-offspring conflict or intersexual conflict for loci influencing offspring production in a non-competitive environment.
Chowdhury, B., Chan, Y.B. and Kravitz, E.A. (2017). Putative transmembrane transporter modulates higher-level aggression in Drosophila. Proc Natl Acad Sci U S A 114: 2373-2378. PubMed ID: 28193893
By selection of winners of dyadic fights for 35 generations, this study generated a hyperaggressive Bully line of flies that almost always win fights against the parental wild-type Canton-S stock. Maintenance of the Bully phenotype is temperature dependent during development: the phenotype is lost when flies are reared at 19 °C. No similar effect is seen with the parent line. This difference served as the basis for RNA-seq experiments which identify a limited number of genes that are differentially expressed by twofold or greater in the Bullies; one of these is a putative transmembrane transporter, CG13646, which shows consistent and reproducible twofold down-regulation in Bullies. The causal effect of this gene on the phenotype was examined with a mutant line for CG13646, and with an RNAi approach. In all cases, reduction in expression of CG13646 by approximately half leads to a hyperaggressive phenotype partially resembling that seen in the Bully flies. This gene is a member of a very interesting family of solute carrier proteins (SLCs), some of which have been suggested as being involved in glutamine/glutamate and GABA cycles of metabolism in excitatory and inhibitory nerve terminals in mammalian systems.

Sanchez-Alcaniz, J. A., Zappia, G., Marion-Poll, F. and Benton, R. (2017). A mechanosensory receptor required for food texture detection in Drosophila. Nat Commun 8: 14192. PubMed ID: 28128210
Textural properties provide information on the ingestibility, digestibility and state of ripeness or decay of sources of nutrition. Compared with the understanding of the chemosensory assessment of food, little is known about the mechanisms of texture detection. This study shows that Drosophila melanogaster can discriminate food texture, avoiding substrates that are either too hard or too soft. Manipulations of food substrate properties and flies' chemosensory inputs indicate that texture preferences are revealed only in the presence of an appetitive stimulus, but are not because of changes in nutrient accessibility, suggesting that animals discriminate the substrates' mechanical characteristics. Texture preference requires NOMPC, a TRP-family mechanosensory channel. NOMPC localizes to the sensory dendrites of neurons housed within gustatory sensilla, and is essential for their mechanosensory-evoked responses. These results identify a sensory pathway for texture detection and reveal the behavioural integration of chemical and physical qualities of food.

Tuesday, March 14th

Goto, M., Toda, N., Shimaji, K., Suong, D. N., Vo, N., Kimura, H., Yoshida, H., Inoue, Y. H. and Yamaguchi, M. (2016). Polycomb-dependent nucleolus localization of Jumonji/Jarid2 during Drosophila spermatogenesis. Spermatogenesis 6(3): e1232023. PubMed ID: 28144496
Drosophila Jumonji/Jarid2 (dJmj) has been identified as a component of Polycomb repressive complex 2. However, it is suggested that dJmj has both PRC-dependent and -independent roles. Subcellular localization of dJmj during spermatogenesis is unknown. Immunocytochemical analyses was performed with specific antibodies to dJmj and tri-methylation at lysine 27 on histone H3 (H3K27me3). Interestingly, dJmj exclusively localizes at nucleolus in the late growth stage. Examination of the dJmj localization in various Polycomb group (PcG) mutant lines at the late growth stage allowed identification of some PcG genes, including Polycomb (Pc), to be responsible for dJmj recruitment to nucleolus. In addition, size of nucleolus was decreased in some of these mutant lines. In a mutant of testis-specific TAF homolog (tTAF) that is responsible for nucleolus localization of Pc, dJmj signals were detected not only at nucleolus but also on the condensed chromatin in the late growth stage. Duolink In situ Proximity ligation assay clarified that Pc interacts with dJmj at nucleolus in the late growth stage. Furthermore, the level of H3K27me3 decreased in nuclei at this stage. Taken together, it is concluded that tTAF is responsible for recruitments of dJmj to nucleolus in the late growth stage that appears to be mediated by Pc. Compartmentalization of dJmj in nucleolus together with some of PcG may be necessary to de-repress the expression of genes required to cellular growth and proliferation in the following meiotic divisions.
Feng, L., Shi, Z. and Chen, X. (2017). Enhancer of polycomb coordinates multiple signaling pathways to promote both cyst and germline stem cell differentiation in the Drosophila adult testis. PLoS Genet 13: e1006571. PubMed ID: 28196077
Stem cells reside in a particular microenvironment known as a niche. The interaction between extrinsic cues originating from the niche and intrinsic factors in stem cells determines their identity and activity. Maintenance of stem cell identity and stem cell self-renewal are known to be controlled by chromatin factors. This study used the Drosophila adult testis which has two adult stem cell lineages, the germline stem cell (GSC) lineage and the cyst stem cell (CySC) lineage, to study how chromatin factors regulate stem cell differentiation. It was found that the chromatin factor Enhancer of Polycomb [E(Pc)] acts in the CySC lineage to negatively control transcription of genes associated with multiple signaling pathways, including JAK-STAT and EGF, to promote cellular differentiation in the CySC lineage. E(Pc) also has a non-cell-autonomous role in regulating GSC lineage differentiation. When E(Pc) is specifically inactivated in the CySC lineage, defects occur in both germ cell differentiation and maintenance of germline identity. Furthermore, compromising Tip60 histone acetyltransferase activity in the CySC lineage recapitulates loss-of-function phenotypes of E(Pc), suggesting that Tip60 and E(Pc) act together, consistent with published biochemical data. In summary, these results demonstrate that E(Pc) plays a central role in coordinating differentiation between the two adult stem cell lineages in Drosophila
Uchida, S., et al. (2017). CRTC1 nuclear translocation following learning modulates memory strength via exchange of chromatin remodeling complexes on the Fgf1 gene. JCell Rep 18(2): 352-366. PubMed ID: 28076781
Evolutionary Homolog Study
Memory is formed by synapse-to-nucleus communication that leads to regulation of gene transcription, but the identity and organizational logic of signaling pathways involved in this communication remain unclear. This study finds that the transcription cofactor CRTC1 (see Drosophila Crtc) is a critical determinant of sustained gene transcription and memory strength in the hippocampus. Following associative learning, synaptically localized CRTC1 is translocated to the nucleus and regulates Fgf1b (see Drosophila Heartless) transcription in an activity-dependent manner. After both weak and strong training, the HDAC3-N-CoR corepressor complex leaves the Fgf1b promoter and a complex involving the translocated CRTC1, phosphorylated CREB (see Drosophila CrebB), and histone acetyltransferase CBP (see Drosophila Nejire) induces transient transcription. Strong training later substitutes KAT5 (see Drosophila Tip60) for CBP, a process that is dependent on CRTC1, but not on CREB phosphorylation. This in turn leads to long-lasting Fgf1b transcription and memory enhancement. Thus, memory strength relies on activity-dependent changes in chromatin and temporal regulation of gene transcription on specific CREB/CRTC1 gene targets.
Capitanio, J.S., Montpetit, B. and Wozniak, R.W. (2017). Human Nup98 regulates the localization and activity of DExH/D-box helicase DHX9. Elife [Epub ahead of print]. PubMed ID: 28221134
Evolutionary Homolog Study:
Beyond their role at nuclear pore complexes, some nucleoporins function in the nucleoplasm. One such nucleoporin, Nup98 (see Drosophila Nup98-96), binds chromatin and regulates gene expression. To gain insight into how Nup98 contributes to this process, this study focused on identifying novel binding partners and understanding the significance of these interactions. The DExH/D-box helicase DHX9 (see Drosophila mle) as an intranuclear Nup98 binding partner (see Nup98 protein-protein interaction network). Various results, including in vitro assays, show that the FG/GLFG region of Nup98 binds to N- and C-terminal regions of DHX9 in an RNA facilitated manner. Importantly, binding of Nup98 stimulates the ATPase activity of DHX9, and a transcriptional reporter assay suggests Nup98 supports DHX9-stimulated transcription. Consistent with these observations, it was found that Nup98 and DHX9 bind interdependently to similar gene loci and their transcripts. Based on these data, the study proposes that Nup98 functions as a co-factor that regulates DHX9 and, potentially, other RNA helicases.

Monday, March 13th

Richhariya, S., Jayakumar, S., Abruzzi, K., Rosbash, M. and Hasan, G. (2017). A pupal transcriptomic screen identifies Ral as a target of store-operated calcium entry in Drosophila neurons. Sci Rep 7: 42586. PubMed ID: 28195208
Transcriptional regulation by Store-operated Calcium Entry (SOCE) is well studied in non-excitable cells. However, the role of SOCE has been poorly documented in neuronal cells with more complicated calcium dynamics. Previous reports demonstrate a requirement for SOCE in neurons that regulate Drosophila flight bouts. This study refined this requirement temporally to the early pupal stage and used RNA-sequencing to identify SOCE mediated gene expression changes in the developing Drosophila pupal nervous system. Down regulation of dStim, the endoplasmic reticular calcium sensor and a principal component of SOCE in the nervous system, alters the expression of 131 genes including Ral, a small GTPase. Disruption of Ral function in neurons impairs flight, whereas ectopic expression of Ral in SOCE-compromised neurons restores flight. Through live imaging of calcium transients from cultured pupal neurons, it was confirmed that Ral does not participate in SOCE, but acts downstream of it. These results identify neuronal SOCE as a mechanism that regulates expression of specific genes during development of the pupal nervous system and emphasizes the relevance of SOCE-regulated gene expression to flight circuit maturation.

Li, A., Hooli, B., Mullin, K., Tate, R.E., Bubnys, A., Kirchner, R., Chapman, B., Hofmann, O., Hide, W. and Tanzi, R.E. (2017). Silencing of the Drosophila ortholog of Sox5 leads to abnormal neuronal development and behavioral impairment. Hum Mol Genet [Epub ahead of print]. PubMed ID: 28186563
SOX5 encodes a transcription factor that is expressed in multiple tissues including heart, lung and brain. Mutations in SOX5 have been previously found in patients with amyotrophic lateral sclerosis (ALS) and developmental delay, intellectual disability and dysmorphic features. To characterize the neuronal role of SOX5, this study silenced the Drosophila ortholog of SOX5, Sox102F, by RNAi in various neuronal subtypes in Drosophila. Silencing of Sox102F leads to misorientated and disorganized michrochaetes, neurons with shorter dendritic arborization (DA) and reduced complexity, diminished larval peristaltic contractions, loss of neuromuscular junction bouton structures, impaired olfactory perception, and severe neurodegeneration in brain. Silencing of SOX5 in human SH-SY5Y neuroblastoma cells results in a significant repression of WNT signaling activity and altered expression of WNT-related genes. Samples of SOX5 variants reveals several variants that show significant association with Alzheimer’s disease disease status. These findings indicate that SOX5 is a novel candidate gene for AD with important role in neuronal function. The genetic findings warrant further studies to identify and characterize SOX5 variants that confer risk for AD, ALS and intellectual disability.

Pankova, K. and Borst, A. (2017). Transgenic line for the identification of cholinergic release sites in Drosophila melanogaster. J Exp Biol [Epub ahead of print]. PubMed ID: 28167805 Summary:
The identification of neurotransmitter type used by a neuron is important for the functional dissection of neuronal circuits. In the model organism Drosophila melanogaster, several methods for discerning the neurotransmitter systems are available. This study expanded the toolbox for the identification of cholinergic neurons by generating a new line FRT-STOP-FRT-VAChT::HA that is a conditional tagged knock-in of the VAChT gene in its endogenous locus. Importantly, in comparison to already available tools for the detection of cholinergic neurons, the FRT-STOP-FRT-VAChT::HA allele also allows for identification of the subcellular localization of the cholinergic presynaptic release sites in a cell-specific manner. The newly generated FRT-STOP-FRT-VAChT::HA line was used to characterize the Mi1 and Tm3 neurons in the fly visual system and found that VAChT is present in the axons of the both cell types, suggesting that Mi1 and Tm3 neurons provide cholinergic input to the elementary motion detectors, the T4 neurons.
Roblodowski, C. and He, Q. (2017). Drosophila Dunc-115 mediates axon projection through actin binding. Invert Neurosci 17(1): 2. PubMed ID: 28124181 Summary:
A central step in organizing the central nervous system development is the growth cone of an axon navigating through guidance cues to reach its specific target. While a great deal of this process has been understood especially in identifying the extracellular guidance cues and their membrane receptors, much less is known about how guidance signals are further relayed to the actin filaments that are central to the mobility of the growth cone. Previous results have shown that Drosophila gene dunc-115 regulates axon projection in the eye and the central nervous system. Furthermore, Dunc-115 has a villin-headpiece (VHD) domain, implying the possibility of binding to actin. To further characterize Dunc-115's functions, this study has identified the isoform Dunc-115L as a possible downstream target in relaying guidance cues further down to the cytoskeleton. Specifically, it was shown that Dunc-115 regulates neural connections in both the eye and the central nervous system in Drosophila and that Dunc-115 contains an actin-binding domain potentially capable of binding to actin filaments. This report shows that Dunc-115 binds to actin via its VHD domain directly, suggesting a possible mechanism for how Dunc-115 relays guidance signals.

Sunday, March 12th

Qiping, S., Haowei, C., Rui, X., Dandan, Z. and Juan, H. (2017). Functional conservation study of polarity protein Crumbs intracellular domain. Yi Chuan 39(1): 32-40. PubMed ID: 28115303
The transmembrane protein Crumbs (Crb) plays key roles in the establishing and maintaining cell apical-basal polarity in epithelial cells by determining the apical plasma membrane identity. Although its intracellular domain contains only 37 amino acids, it is absolutely essential for its function. In Drosophila, mutations in this intracellular domain result in severe defects in epithelial polarity and abnormal embryonic development. The intracellular domain of Crb shows high homology across species from Drosophila to Mus musculus and Homo sapiens. However, the intracellular domains of the two Crb proteins in C. elegans are rather divergent from those of Drosophila and mammals, raising the question on whether the function of the intracellular domain of the Crb protein is conserved in C. elegans. Using genomic engineering approach, this study replaced the intracellular domain of the Drosophila Crb with that of C. elegans Crb2 (CeCrb2), which has extremely low homology with those from the Crb proteins of Drosophila and mammals. Surprisingly, substituting the intracellular domain of Drosophila Crb with that of CeCrb2 did not cause any abnormalities in development of the Drosophila embryo, in terms of expression and localization of Crb and other polarity proteins and apical-basal polarity in embryonic epithelial cells. These results support the notion that despite their extensive sequence variations, all functionally critical amino acid residues and motifs of the intercellular domain of Crb proteins are fully conserved between Drosophila and C. elegans.
Raza, Q. S., Vanderploeg, J. L. and Jacobs, J. R. (2017). Matrix Metalloproteinases are required for membrane motility and lumenogenesis during Drosophila heart development. PLoS One 12(2): e0171905. PubMed ID: 28192468
Matrix Metalloproteinases (Mmps) degrade glycoproteins and proteoglycans of the extracellular matrix (ECM) or cell surface and are crucial for morphogenesis. Drosophila genome encodes two copies of Mmps, Mmp1 and Mmp2 whereas in humans up to 25 Mmps have been identified with overlapping functions. This study investigated the role of Mmps during embryonic heart development in Drosophila. The two Mmps in Drosophila are shown to have distinct and overlapping roles in cell motility, cell adhesion and cardiac lumenogenesis. Mmp1 and Mmp2 promote Leading Edge membrane dynamics of cardioblasts during collective migration. Mmp2 is essential for cardiac lumen formation, and mutants generate a cardia bifida phenotype. Mmp1 is required for luminal expansion. Mmp1 and Mmp2 both localise to the basal domains of cardiac cells, however, occupy non-overlapping domains apically. Mmp1 and Mmp2 regulate the proteoglycan composition and size of the apical and basal ECM, yet only Mmp2 is required to restrict ECM assembly to the lumen. Mmp1 negatively regulates the size of the adhesive Cadherin cell surface domain, whereas in a complementary fashion, Mmp2 negatively regulates the size of the Integrin-ECM domain and thereby prescribes the domain to establish and restrict Slit morphogen signalling. Inhibition of Mmp activity through ectopic expression of Tissue Inhibitor of Metalloproteinase in the ectoderm blocks lumen formation. Therefore, Mmp expression and function identifies ECM differentiation and remodelling as a key element for cell polarisation and organogenesis.
Doubrovinski, K., Swan, M., Polyakov, O. and Wieschaus, E. F. (2017). Measurement of cortical elasticity in Drosophila melanogaster embryos using ferrofluids. Proc Natl Acad Sci U S A 114(5): 1051-1056. PubMed ID: 28096360
Many models of morphogenesis are forced to assume specific mechanical properties of cells, because the actual mechanical properties of living tissues are largely unknown. This study measured the rheology of epithelial cells in the cellularizing Drosophila embryo by injecting magnetic particles and studying their response to external actuation. It was established that, on timescales relevant to epithelial morphogenesis, the cytoplasm is predominantly viscous, whereas the cellular cortex is elastic. The timescale of elastic stress relaxation has a lower bound of 4 min, which is comparable to the time required for internalization of the ventral furrow during gastrulation. The cytoplasm was measured to be approximately 103-fold as viscous as water. Elasticity was shown to depend on the actin cytoskeleton, and these results are discussed as to how they relate to existing mechanical models of morphogenesis.
Zhang, G., Xie, Y., Zhou, Y., Xiang, C., Chen, L., Zhang, C., Hou, X., Chen, J., Zong, H. and Liu, G. (2017).. p53 pathway is involved in cell competition during mouse embryogenesis. Proc Natl Acad Sci U S A. PubMed ID: 28049824
Evolutionary Homolog Study
The function of tumor suppressor p53 (see Drosophila p53) has been under intense investigation. Murine double minute (MDM)2 and MDM4 are two major negative regulators of p53. This study used the strategy of haploinsufficiency of Mdm2 and Mdm4 to induce mild p53 activation in vivo and found that Mdm2+/-Mdm4+/- double-heterozygous mice exhibited normal embryogenesis. However, closer examination demonstrated that the Mdm2+/-Mdm4+/- cells exhibited a growth disadvantage and were outcompeted during development in genetic mosaic embryos that contained wild-type cells. Further study indicated the out-competition phenotype was dependent on the levels of p53. These observations revealed that cells with mild p53 activation were less fit and exhibited altered fates in a heterotypic environment, resembling the cell competition phenomenon first uncovered in Drosophila. By marking unfit cells for elimination, p53 may exert its physiological role to ensure organ and animal fitness.

Saturday, March 11th

Malmanche, N., Dourlen, P., Gistelinck, M., Demiautte, F., Link, N., Dupont, C., Vanden Broeck, L., Werkmeister, E., Amouyel, P., Bongiovanni, A., Bauderlique, H., Moechars, D., Royou, A., Bellen, H. J., Lafont, F., Callaerts, P., Lambert, J. C. and Dermaut, B. (2017). Developmental expression of 4-Repeat-Tau induces neuronal aneuploidy in Drosophila tauopathy models. Sci Rep 7: 40764. PubMed ID: 28112163
Tau-mediated neurodegeneration in Alzheimer's disease and tauopathies is generally assumed to start in a normally developed brain. However, several lines of evidence suggest that impaired Tau isoform expression during development could affect mitosis and ploidy in post-mitotic differentiated tissue. Interestingly, the relative expression levels of Tau isoforms containing either 3 (3R-Tau) or 4 repeats (4R-Tau) play an important role both during brain development and neurodegeneration. This study used genetic and cellular tools to study the link between 3R and 4R-Tau isoform expression, mitotic progression in neuronal progenitors and post-mitotic neuronal survival. The results illustrated that the severity of Tau-induced adult phenotypes depends on 4R-Tau isoform expression during development. As recently described, a mitotic delay was observed in 4R-Tau expressing cells of larval eye discs and brains. Live imaging revealed that the spindle undergoes a cycle of collapse and recovery before proceeding to anaphase. Furthermore, a high level of aneuploidy was found in post-mitotic differentiated tissue. Finally, it was shown that overexpression of wild type and mutant 4R-Tau isoform in neuroblastoma SH-SY5Y cell lines is sufficient to induce monopolar spindles. Taken together, these results suggested that neurodegeneration could be in part linked to neuronal aneuploidy caused by 4R-Tau expression during brain development.
Mansilla, A., Chaves-Sanjuan, A., Campillo, N. E., Semelidou, O., Martinez-Gonzalez, L., Infantes, L., Gonzalez-Rubio, J. M., Gil, C., Conde, S., Skoulakis, E. M., Ferrus, A., Martinez, A. and Sanchez-Barrena, M. J. (2017). Interference of the complex between NCS-1 and Ric8a with phenothiazines regulates synaptic function and is an approach for fragile X syndrome. Proc Natl Acad Sci U S A 114(6): E999-e1008. PubMed ID: 28119500
The protein complex formed by the Ca2+ sensor neuronal calcium sensor 1 (NCS-1) and the guanine exchange factor protein Ric8a (see Drosophila Ric8) coregulates synapse number and probability of neurotransmitter release, emerging as a potential therapeutic target for diseases affecting synapses, such as fragile X syndrome (FXS), the most common heritable autism disorder. Using crystallographic data and the virtual screening of a chemical library, this study identified a set of heterocyclic small molecules as potential inhibitors of the NCS-1/Ric8a interaction. The aminophenothiazine FD44 interferes with NCS-1/Ric8a binding, and it restores normal synapse number and associative learning in a Drosophila FXS model. The synaptic effects elicited by FD44 feeding are consistent with the genetic manipulation of NCS-1. The crystal structure of NCS-1 bound to FD44 and the structure-function studies performed with structurally close analogs explain the FD44 specificity and the mechanism of inhibition, in which the small molecule stabilizes a mobile C-terminal helix inside a hydrophobic crevice of NCS-1 to impede Ric8a interaction. This study shows the drugability of the NCS-1/Ric8a interface and uncovers a suitable region in NCS-1 for development of additional drugs of potential use on FXS and related synaptic disorders.
M'Angale, P. G. and Staveley, B. E. (2016). Overexpression of Buffy enhances the loss of parkin and suppresses the loss of Pink1 phenotypes in Drosophila. Genome: 1-7 [Epub ahead of print]. PubMed ID: 28106473
Mutations in parkin (PARK2) and Pink1 (PARK6) are responsible for autosomal recessive forms of early onset Parkinson's disease (PD). Attributed to the failure of neurons to clear dysfunctional mitochondria, loss of gene expression leads to loss of nigrostriatal neurons. The Pink1/parkin pathway plays a role in the quality control mechanism aimed at eliminating defective mitochondria, and the failure of this mechanism results in a reduced lifespan and impaired locomotor ability, among other phenotypes. Inhibition of parkin or Pink1 through the induction of stable RNAi transgene in the Ddc-Gal4-expressing neurons results in such phenotypes to model PD. To further evaluate the effects of the overexpression of the Bcl-2 homologue Buffy, this study analysed lifespan and climbing ability in both parkin-RNAi- and Pink1-RNAi-expressing flies. In addition, the effect of Buffy overexpression upon parkin-induced developmental eye defects was examined through GMR-Gal4-dependent expression. Curiously, Buffy overexpression produced very different effects: the parkin-induced phenotypes were enhanced, whereas the Pink1-enhanced phenotypes were suppressed. Interestingly, the overexpression of Buffy along with the inhibition of parkin in the neuron-rich eye results in the suppression of the developmental eye defects.
Hong, Y. G., Roh, S., Paik, D. and Jeong, S. (2017). Development of a reporter system for in vivo monitoring of γ-Secretase activity in Drosophila. Mol Cells 40(1): 73-81. PubMed ID: 28152299
The γ-secretase complex (see Presenilin) represents an evolutionarily conserved family of transmembrane aspartyl proteases that cleave numerous type-I membrane proteins, including the β-amyloid precursor protein (APP) and the receptor Notch. All known rare mutations in APP and the γ-secretase catalytic component, presenilin, which lead to increased amyloid β peptide production, are responsible for early-onset familial Alzheimer's disease. β-amyloid protein precursor-like (APPL) is the Drosophila ortholog of human APP. This study created Notch- and APPL-based Drosophila reporter systems for in vivo monitoring of γ-secretase activity. Ectopic expression of the Notch- and APPL-based chimeric reporters in wings results in vein truncation phenotypes. Reporter-mediated vein truncation phenotypes are enhanced by the Notch gain-of-function allele and suppressed by RNAi-mediated knockdown of presenilin. Furthermore, apoptosis was found to partly contribute to the vein truncation phenotypes of the APPL-based reporter, but not to the vein truncation phenotypes of the Notch-based reporter. Taken together, these results suggest that both in vivo reporter systems provide a powerful genetic tool to identify genes that modulate γ-secretase activity and/or APPL metabolism.
Kumar, A., Christian, P. K., Panchal, K., Guruprasad, B. R. and Tiwari, A. K. (2017). Supplementation of spirulina (Arthrospira platensis) improves lifespan and locomotor activity in paraquat-sensitive DJ-1βΔ93 flies, a Parkinson's disease model in Drosophila melanogaster. J Diet Suppl: 1-16. PubMed ID: 28166438
Spirulina (Arthrospira platensis) is a cyanobacterium (blue-green alga) consumed by humans and other animals because of its nutritional values and pharmacological properties. Apart from high protein contents, it also contains high levels of antioxidant and anti-inflammatory compounds, such as carotenoids, β-carotene, phycocyanin, and phycocyanobilin, indicating its possible pharmaco-therapeutic utility. In the present study using DJ-1βΔ93 flies, a Parkinson's disease model in Drosophila, this study has demonstrated the therapeutic effect of spirulina and its active component C-phycocyanin (C-PC) in the improvement of lifespan and locomotor behavior. The findings indicate that dietary supplementation of spirulina significantly improves the lifespan and locomotor activity of paraquat-fed DJ-1βΔ93 flies. Furthermore, supplementation of spirulina and C-PC individually and independently reduced the cellular stress marked by deregulating the expression of heat shock protein 70 and Jun-N-terminal kinase signaling in DJ-1βΔ93 flies. A significant decrease in superoxide dismutase and catalase activities in spirulina-fed DJ-1βΔ93 flies tends to indicate the involvement of antioxidant properties associated with spirulina in the modulation of stress-induced signaling and improvement in lifespan and locomotor activity in Drosophila DJ-1βΔ93 flies. These results suggest that antioxidant boosting properties of spirulina can be used as a nutritional supplement for improving the lifespan and locomotor behavior in Parkinson's disease.
Moskalev, A., Shaposhnikov, M., Proshkina, E., Belyi, A., Fedintsev, A., Zhikrivetskaya, S., Guvatova, Z., Sadritdinova, A., Snezhkina, A., Krasnov, G. and Kudryavtseva, A. (2016). The influence of pro-longevity gene Gclc overexpression on the age-dependent changes in Drosophila transcriptome and biological functions. BMC Genomics 17(Suppl 14): 1046. PubMed ID: 28105938
Transcriptional changes that contribute to the organism's longevity and prevent the age-dependent decline of biological functions are not well understood. This study overexpressed pro-longevity gene encoding glutamate-cysteine ligase catalytic subunit (Gclc) and analyzed age-dependent changes in transcriptome that associated with the longevity, stress resistance, locomotor activity, circadian rhythmicity, and fertility. The life extension effect of neuronal overexpression of the Gclc gene were reproduced, and its influence on the age-depended dynamics of transcriptome and biological functions such as fecundity, spontaneous locomotor activity and circadian rhythmicity were investigated, as well as on the resistance to oxidative, proteotoxic and osmotic stresses. It was shown that Gclc overexpression reduces locomotor activity in the young and middle ages compared to control flies. Gclc overexpression slowed down the age-dependent decline of locomotor activity and circadian rhythmicity, and resistance to stress treatments. Gclc level demonstrated associations with the expression of genes involved in a variety of cellular processes including Jak-STAT, MAPK, FOXO, Notch, mTOR, TGF-beta signaling pathways, translation, protein processing in endoplasmic reticulum, proteasomal degradation, glycolysis, oxidative phosphorylation, apoptosis, regulation of circadian rhythms, differentiation of neurons, synaptic plasticity and transmission. This study revealed that Gclc overexpression induces transcriptional changes associated with the lifespan extension and uncovered pathways that may be associated with the age-dependent decline of biological functions.

Friday, March 10th

Schwenke, R.A. and Lazzaro, B.P. (2017). Juvenile Hormone suppresses resistance to infection in mated female Drosophila melanogaster. Curr Biol 27: 596-601. PubMed ID: 28190728
Hormonal signaling provides metazoans with the ability to regulate development, growth, metabolism, immune defense, and reproduction in response to internal and external stimuli. The use of hormones as central regulators of physiology makes them prime candidates for mediating allocation of resources to competing biological functions (i.e., hormonal pleiotropy). In animals, reproductive effort often results in weaker immune responses, and this reduction is sometimes linked to hormone signaling. In the fruit fly, Drosophila melanogaster, mating and the receipt of male seminal fluid proteins results in reduced resistance to a systemic bacterial infection. This study evaluated whether the immunosuppressive effect of reproduction in female D. melanogaster is attributable to the endocrine signal juvenile hormone (JH), which promotes the development of oocytes and the synthesis and deposition of yolk protein. Previous work has implicated JH as immunosuppressive, and the male seminal fluid protein Sex Peptide (SP) activates JH biosynthesis in female D. melanogaster after mating. It was found that transfer of SP activates synthesis of JH in the mated female, which in turn suppresses resistance to infection through the receptor germ cell expressed (gce). Mated females are more likely to die from infection, suffer higher pathogen burdens, and are less able to induce their immune responses. All of these deficiencies are rescued when JH signaling is blocked. Thus, hormonal signaling is important for regulating immune system activity and, more generally, for governing trade-offs between physiological processes.

Jonchere, V., Alqadri, N., Herbert, J., Dodgson, L., Mason, D., Messina, G., Falciani, F. and Bennett, D. (2017). Transcriptional responses to hyperplastic MRL signalling in Drosophila. Open Biol 7(2). PubMed ID: 28148822
Recent work has implicated the actin cytoskeleton in tissue size control and tumourigenesis, but how changes in actin dynamics contribute to hyperplastic growth is still unclear. Overexpression of Pico, the only Drosophila Mig-10/RIAM/Lamellipodin (MRL) adapter protein family member, has been linked to tissue overgrowth via its effect on the myocardin-related transcription factor (Mrtf), an F-actin sensor capable of activating serum response factor (SRF). Transcriptional changes induced by acute Mrtf/SRF signalling have been largely linked to actin biosynthesis and cytoskeletal regulation. However, by RNA profiling, the common response to chronic mrtf and pico overexpression in wing discs was found to upregulate ribosome protein and mitochondrial genes, which are conserved targets for Mrtf/SRF and are known growth drivers. Consistent with their ability to induce a common transcriptional response and activate SRF signalling in vitro, both pico and mrtf were found to stimulate expression of an SRF-responsive reporter gene in wing discs. In a functional genetic screen, deterin, which encodes Drosophila Survivin, was found to be a putative Mrtf/SRF target that is necessary for pico-mediated tissue overgrowth by suppressing proliferation-associated cell death. Taken together, these findings raise the possibility that distinct targets of Mrtf/SRF may be transcriptionally induced depending on the duration of upstream signalling.
Ling, X., Huang, Q., Xu, Y., Jin, Y., Feng, Y., Shi, W., Ye, X., Lin, Y., Hou, L. and Lin, X. (2017). The deubiquitinating enzyme Usp5 regulates Notch and RTK signaling during Drosophila eye development. FEBS Lett [Epub ahead of print]. PubMed ID: 28140449
Usp5 belongs to the USP family of deubiquitinating enzymes (DUBs), which comprises the largest class of DUBs. Loss of Usp5 has been shown to impair development of photoreceptors in Drosophila eyes, but the detailed mechanism remained unclear. This study demonstrated that Usp5 regulates both Notch and receptor tyrosine kinase (RTK) signaling. Loss of Usp5 results in upregulation of Notch signaling and downregulation of RTK signaling, leading to impaired photoreceptor development. Moreover, genetic rescue experiments with Su(H) or Notch RNAi indicate that they mediate the regulation of RTK signaling by Usp5. This study provides mechanistic insight into how Usp5 regulates photoreceptor differentiation by Notch and RTK signaling in the Drosophila eye.
Mayfield, J. E., et al. (2017). Mapping the Phosphorylation Pattern of Drosophila melanogaster RNA Polymerase II Carboxyl-Terminal Domain Using Ultraviolet Photodissociation Mass Spectrometry. ACS Chem Biol 12(1): 153-162. PubMed ID: 28103682
Phosphorylation of the C-terminal domain of RNA polymerase II (CTD) plays an essential role in eukaryotic transcription by recruiting transcriptional regulatory factors to the active polymerase. However, the scarcity of basic residues and repetitive nature of the CTD sequence impose a huge challenge for site-specific characterization of phosphorylation, hindering understanding of this crucial biological process. This study applied LC-UVPD-MS methods to analyze post-translational modification along native sequence CTDs. Application of this method to the Drosophila melanogaster CTD reveals the phosphorylation pattern of this model organism for the first time. The divergent nature of fly CTD allowed derivation of rules defining how flanking residues affect phosphorylation choice by CTD kinases. The data support the use of LC-UVPD-MS to decipher the CTD code and determine rules that program its function.
Weber, U. and Mlodzik, M. (2017). APC/CFzr/Cdh1-Dependent Regulation of Planar Cell Polarity Establishment via Nek2 Kinase Acting on Dishevelled. Dev Cell 40(1): 53-66. PubMed ID: 28041906
The Anaphase-Promoting Complex/Cyclosome (APC/C) is an E3 ubiquitin ligase, well known for its role in cell-cycle progression. However, it has been linked to additional functions, mainly in neuronal contexts, when using the co-activator Cdh1/Fzr. This study indicates a post-mitotic requirement for the APC/CFzr/Cdh1 in epithelial cell patterning and planar cell polarity (PCP) in Drosophila. PCP signaling is critical for development by establishing cellular asymmetries and orientation within the plane of an epithelium, via differential localization of distinct complexes of core PCP factors. Loss of APC/C function leads to reduced levels of Dishevelled (Dsh), a core PCP factor. The effect of APC/C on Dsh is mediated by Nek2 kinase, which can phosphorylate Dsh and is a direct APC/CFzr/Cdh1 substrate. This study has thus uncovered a pathway of regulation whereby APC/CFzr/Cdh1 negatively regulates Nek2, which negatively regulates Dsh, to ensure its proper stoichiometric requirement and localization during PCP establishment.
Posfai, E., Petropoulos, S., de Barros, F. R., Schell, J. P., Jurisica, I., Sandberg, R., Lanner, F. and Rossant, J. (2017). Position- and Hippo signaling-dependent plasticity during lineage segregation in the early mouse embryo. Elife 6. PubMed ID: 28226240
Evolutionary Homolog Study
The segregation of the trophectoderm (TE) from the inner cell mass (ICM) in the mouse blastocyst is determined by position-dependent Hippo signaling. However, the window of responsiveness to Hippo signaling, the exact timing of lineage commitment and the overall relationship between cell commitment and global gene expression changes are still unclear. Single-cell RNA sequencing during lineage segregation revealed that the TE transcriptional profile stabilizes earlier than the ICM and prior to blastocyst formation. Using quantitative Cdx2-eGFP (see Drosophila Caudal) expression as a readout of Hippo signaling activity, this study assessed the experimental potential of individual blastomeres based on their level of Cdx2-eGFP expression and correlated potential with gene expression dynamics. TE specification and commitment was found to coincide and occur at the time of transcriptional stabilization, whereas ICM cells still retain the ability to regenerate TE up to the early blastocyst stage. Plasticity of both lineages is coincident with their window of sensitivity to Hippo signaling.

Thursday, March 9th

Zhang, R., Deng, P., Jacobson, D. and Li, J.B. (2017). Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing. PLoS Genet [Epub ahead of print]. PubMed ID: 28166241
Adenosine-to-inosine RNA editing (see Adar) diversifies the transcriptome and promotes functional diversity, particularly in the brain. A plethora of editing sites has been recently identified; however, how they are selected and regulated and which are functionally important are largely unknown. This study shows the cis-regulation and stepwise selection of RNA editing during Drosophila evolution and pinpoints a large number of functional editing sites. It was found that the establishment of editing and variation in editing levels across Drosophila species are largely explained and predicted by cis-regulatory elements. Furthermore, editing events that arise early in the species tree tend to be more highly edited in clusters and enriched in slowly-evolved neuronal genes, thus suggesting that the main role of RNA editing is for fine-tuning neurological functions. While nonsynonymous editing events have been long recognized as playing a functional role, in addition to nonsynonymous editing sites, a large fraction of 3'UTR editing sites is evolutionarily constrained, highly edited, and thus likely functional. These 3'UTR editing events can alter mRNA stability and affect miRNA binding and thus highlight the functional roles of noncoding RNA editing.

Lopez-Maestre, H., Carnelossi, E. A., Lacroix, V., Burlet, N., Mugat, B., Chambeyron, S., Carareto, C. M. and Vieira, C. (2017). Identification of misexpressed genetic elements in hybrids between Drosophila-related species. Sci Rep 7: 40618. PubMed ID: 28091568
Crosses between close species can lead to genomic disorders, often considered to be the cause of hybrid incompatibility, one of the initial steps in the speciation process. How these incompatibilities are established and what are their causes remain unclear. To understand the initiation of hybrid incompatibility, reciprocal crosses were performed between two species of Drosophila (D. mojavensis and D. arizonae) that diverged less than 1 Mya. A genome-wide transcriptomic analysis was performed on ovaries from parental lines and on hybrids from reciprocal crosses. Using an innovative procedure of co-assembling transcriptomes, it was shown that parental lines differ in the expression of their genes and transposable elements. Reciprocal hybrids presented specific gene categories and few transposable element families misexpressed relative to the parental lines. Because TEs are mainly silenced by piwi-interacting RNAs (piRNAs), it was hypothesized that in hybrids the deregulation of specific TE families is due to the absence of such small RNAs. Small RNA sequencing confirmed the hypothesis, and it is therefore proposed that TEs can indeed be major players of genome differentiation and be implicated in the first steps of genomic incompatibilities through small RNA regulation.
Karam, J.A., Parikh, R.Y., Nayak, D., Rosenkranz, D. and Gangaraju, V.K. (2017). Co-chaperone Hsp70/Hsp90 organizing protein (Hop) is required for transposon silencing and piRNA biogenesis. J Biol Chem [Epub ahead of print]. PubMed ID: 28193840
piRNAs are 26-30nt germ-line specific small non-coding RNAs that have evolutionarily conserved function in mobile genetic element (transposons) silencing and maintenance of genome integrity. Drosophila Hsp70/90 Organizing Protein Homolog (Hop), a co-chaperone, interacts with piRNA binding protein Piwi and mediates silencing of phenotypic variations. However, it is not known if Hop has a direct role in piRNA biogenesis and transposon silencing. This study shows that knockdown of Hop in the germ-line nurse cells (GLKD) of Drosophila ovaries leads to activation of transposons. Hop GLKD females can lay eggs at the same rate as wild type counterparts but the eggs do not hatch into larvae. Hop GLKD leads to the accumulation of γ-H2Av foci in the germline indicating increased DNA damage in the ovary. Hop GLKD induced transposon up-regulation is due to inefficient piRNA biogenesis. Based on these results, the study concludes that Hop is a critical component of piRNA pathway and it maintains genome integrity by silencing transposons.

Li, S., Shen, L., Sun, L., Xu, J., Jin, P., Chen, L. and Ma, F. (2017). Small RNA-Seq analysis reveals microRNA-regulation of the Imd pathway during Escherichia coli infection in Drosophila. Dev Comp Immunol [Epub ahead of print]. PubMed ID: 28069431
Drosophila have served as a model for research on innate immunity for decades. However, knowledge of the post-transcriptional regulation of immune gene expression by microRNAs (miRNAs) remains rudimentary. Using small RNA-seq and bioinformatics analysis, this study identified 67 differentially expressed miRNAs in Drosophila infected with Escherichia coli compared to injured flies at three time-points. Twenty-one of these miRNAs were potentially involved in the regulation of Imd pathway-related genes. Strikingly, based on UAS-miRNAs line screening and Dual-luciferase assay, miR-9a and miR-981 both negatively regulated Drosophila antibacterial defenses and decreased the level of the antibacterial peptide, Diptericin. Taken together, these data support the involvement of miRNAs in the regulation of the Drosophila Imd pathway.

Wednesday, March 8th

Lim, B., Levine, M. and Yamakazi, Y. (2017). Transcriptional pre-patterning of Drosophila gastrulation. Curr Biol 27(2): 286-290. PubMed ID: 28089518
Gastrulation of the Drosophila embryo is one of the most intensively studied morphogenetic processes in animal development. Particular efforts have focused on the formation of the ventral furrow, whereby approximately 1,000 presumptive mesoderm cells exhibit coordinated apical constrictions that mediate invagination. Apical constriction depends on a Rho GTPase signaling pathway (T48/Fog) that is deployed by the developmental regulatory genes twist and snail. It is thought that coordinate mesoderm constriction depends on high levels of myosin along the ventral midline, although the basis for this localization is uncertain. This study employed newly developed quantitative imaging methods to visualize the transcriptional dynamics of two key components of the Rho signaling pathway in living embryos, T48 and Fog. Both genes display dorsoventral (DV) gradients of expression due to differential timing of transcription activation. Transcription begins as a narrow stripe of two or three cells along the ventral midline, followed by progressive expansions into more lateral regions. Quantitative image analyses suggest that these temporal gradients produce differential spatial accumulations of t48 and fog mRNAs along the DV axis, similar to the distribution of myosin activity. It is therefore proposed that the transcriptional dynamics of t48 and fog expression foreshadow the coordinated invagination of the mesoderm at the onset of gastrulation.
Perez Ipina, E. and Ponce Dawson, S. (2017). The effect of reactions on the formation and readout of the gradient of Bicoid. T. Phys Biol.[Epub ahead of print]. PubMed ID: 28054512
During early development, the establishment of gradients of transcriptional factors determines the patterning of cell fates. The case of Bicoid (Bcd) in Drosophila melanogaster embryos is well documented and studied. There are still controversies as to whether SDD models in which Bcd is Synthesized at one end, then Diffuses and is Degraded can explain the gradient formation within the timescale observed experimentally. The Bcd gradient is observed in embryos that express a Bicoid-eGFP fusion protein (Bcd-GFP) which cannot differentiate if Bcd is freely diffusing or bound to immobile sites. This work analyzed an SDID model that includes the interaction of Bcd with binding sites. The resulting full reaction-diffusion system was simulated numerically in a cylindrical domain using previously determined biophysical parameters and a simplified version of the Bcd source. In this way solutions were obtained that depend on the spatial location approximately as observed experimentally and that reach such dependence at a time that is also compatible with the experimental observations. Analyzing the differences between the free and bound Bcd distributions it was observed that the latter spans over a longer lengthscale. It is concluded that deriving the lengthscale from the distribution of Bcd-GFP can lead to an overestimation of the gradient lengthscale and of the Hill coefficient that relates the concentrations of Bcd and of the protein, Hunchback, whose production is regulated by Bcd.
Lefebvre, F. A., Benoit Bouvrette, L. P., Bergalet, J. and Lecuyer, E. (2017). Biochemical fractionation of time-resolved Drosophila embryos reveals similar transcriptomic alterations in replication checkpoint and histone mRNA processing mutants. J Mol Biol [Epub ahead of print]. PubMed ID: 28167048
In higher eukaryotes, maternally provided gene products drive the initial stages of embryogenesis until the zygotic transcriptional program takes over, a developmental process called the midblastula transition (MBT). In addition to zygotic genome activation, the MBT involves alterations in cell-cycle length and the implementation of DNA damage/replication checkpoints that serve to monitor genome integrity. Previous work has shown that mutations affecting histone mRNA metabolism or DNA replication checkpoint factors severely impact developmental progression through the MBT, prompting this study to characterize and contrast the transcriptomic impact of these genetic perturbations. This study defined gene expression profiles that mark early embryogenesis in Drosophila through transcriptomic analyses of developmentally staged (early syncytial vs late blastoderm) and biochemically fractionated (nuclear vs cytoplasmic) wild type embryos. The transcriptomic profiles were compared of loss-of-function mutants of the Chk1/Grapes replication checkpoint kinase and the Stem Loop Binding Protein (SLBP), a key regulator of replication-dependent histone mRNAs. This analysis of RNA spatial and temporal distribution during embryogenesis offers new insights into the dynamics of early embryogenesis. In addition, it was found that grp and Slbp mutant embryos display profound and highly similar defects in gene expression, most strikingly in zygotic gene expression, compromising the transition from a maternal to a zygotic regulation of development.
Wang, C., Wang, M., Arrington, J., Shan, T., Yue, F., Nie, Y., Tao, W. A. and Kuang, S. (2017). Ascl2 inhibits myogenesis by antagonizing the transcriptional activity of myogenic regulatory factors. Development 144(2): 235-247. PubMed ID: 27993983
Evolutionary Homolog Study
Myogenic regulatory factors (MRFs), including Myf5, MyoD and Myog. (see Drosophila Nautilus), are muscle-specific transcription factors that orchestrate myogenesis. Although MRFs are essential for myogenic commitment and differentiation, timely repression of their activity is necessary for the self-renewal and maintenance of muscle stem cells (satellite cells). This study defines Ascl2 (see Drosophila Achaete) as a novel inhibitor of MRFs. During mouse development, Ascl2 is transiently detected in a subpopulation of Pax7+ MyoD+ progenitors (myoblasts) that become Pax7+ MyoD- satellite cells prior to birth, but is not detectable in postnatal satellite cells. Ascl2 knockout in embryonic myoblasts decreases both the number of Pax7+ (see Drosophila Paired) cells and the proportion of Pax7+ MyoD- cells. Conversely, overexpression of Ascl2 inhibits the proliferation and differentiation of cultured myoblasts and impairs the regeneration of injured muscles. Ascl2 competes with MRFs for binding to E-boxes in the promoters of muscle genes, without activating gene transcription. Ascl2 also forms heterodimers with classical E-proteins to sequester their transcriptional activity on MRF genes. Accordingly, MyoD or Myog expression rescues myogenic differentiation despite Ascl2 overexpression. Ascl2 expression is regulated by Notch signaling, a key governor of satellite cell self-renewal. These data demonstrate that Ascl2 inhibits myogenic differentiation by targeting MRFs and facilitates the generation of postnatal satellite cells.

Tuesday, March 7th

Shukla, J.P., Deshpande, G. and Shashidhara, L.S. (2017). Ataxin-2 binding protein 1 is a context-specific positive regulator of Notch signaling during neurogenesis in Drosophila melanogaster. Development [Epub ahead of print]. PubMed ID: 28174239
The role of Notch pathway during lateral inhibition underlying binary cell fate choice is extensively studied, although context-specificity that generates diverse outcomes is relatively less well understood. In the peripheral nervous system of Drosophila melanogaster, differential Notch signaling between cells of proneural cluster orchestrates sensory organ specification. This study reports functional analysis of Drosophila Ataxin2 binding protein1 (dA2BP1) during this process. It's human orthologue A2BP1 is linked to type 2 Spinocerebellar ataxia and other complex neuronal disorders. Downregulation of dA2BP1 in the proneural cluster increases adult sensory bristle number whereas it's over-expression results in loss of bristles. dA2BP1was found to regulate sensory organ specification by potentiating Notch signaling. Supporting its direct involvement, biochemical analysis showed that dA2BP1 is part of the Suppressor of Hairless (Su(H)) complex both in the presence and absence of Notch. However, in the absence of Notch signaling, the dA2BP1 interacting fraction of Su(H) does not associate with the repressor proteins, Groucho and CtBP. Based on these data the study proposes a model explaining requirement of dA2BP1 as a positive regulator of Notch, whose activity is context-specific.

Fu, Y., Zhu, J. Y., Zhang, F., Richman, A., Zhao, Z. and Han, Z. (2017). Comprehensive functional analysis of Rab GTPases in Drosophila nephrocytes. Cell Tissue Res [Epub ahead of print]. PubMed ID: 28180992
The Drosophila nephrocyte is a critical component of the fly renal system and bears structural and functional homology to podocytes and proximal tubule cells of the mammalian kidney. Nephrocytes are highly active in endocytosis and vesicle trafficking. Rab GTPases regulate endocytosis and trafficking but specific functions of nephrocyte Rabs remain undefined. This study analyzed Rab GTPase expression and function in Drosophila nephrocytes and found that 11 out of 27 Drosophila Rabs were required for normal activity. Rabs 1, 5, 7, 11 and 35 were most important. Gene silencing of the nephrocyte-specific Rab5 eliminated all intracellular vesicles and the specialized plasma membrane structures essential for nephrocyte function. Rab7 silencing dramatically increased clear vacuoles and reduced lysosomes. Rab11 silencing increased lysosomes and reduced clear vacuoles. These results suggest that Rab5 mediates endocytosis that is essential for the maintenance of functionally critical nephrocyte plasma membrane structures and that Rabs 7 and 11 mediate alternative downstream vesicle trafficking pathways leading to protein degradation and membrane recycling, respectively. Elucidating molecular pathways underlying nephrocyte function has the potential to yield important insights into human kidney cell physiology and mechanisms of cell injury that lead to disease.
Guisoni, N., Martinez-Corral, R., Garcia Ojalvo, J. and de Navascues, J. (2017). Diversity of fate outcomes in cell pairs under lateral inhibition. Development [Epub ahead of print]. PubMed ID: 28174242
Cell fate determination by lateral inhibition via Notch/Delta signalling has been extensively studied. Most formalised models consider Notch/Delta interactions in fields of cells, with parameters that typically lead to symmetry breaking of signalling states between neighbouring cells, commonly resulting in salt-and-pepper fate patterns. This study considers the case of signalling between isolated cell pairs. The bifurcation properties of a standard mathematical model of lateral inhibition was found to lead to stable symmetric signalling states. This model was applied to the adult intestinal stem cell (ISC) of Drosophila, whose fate is stochastic but dependent on the Notch/Delta pathway. A correlation was observed between signalling state in cell pairs and their contact area. This behaviour is intrepeted in terms of the properties of the model in the presence of population variability in contact areas, which affects the effective signalling threshold of individual cells. The results suggest that the dynamics of Notch/Delta signalling can contribute to explain stochasticity in stem cell fate decisions, and that the standard model for lateral inhibition can account for a wider range of developmental outcomes than previously considered.
Kakuda, S. and Haltiwanger, R. S. (2017). Deciphering the Fringe-Mediated Notch Code: Identification of Activating and Inhibiting Sites Allowing Discrimination between Ligands. Dev Cell 40(2): 193-201. PubMed ID: 28089369
Evolutionary Homolog Study
Fringe proteins (see Drosophila Fringe) are beta3-N-acetylglucosaminyltransferases that modulate Notch activity by modifying O-fucose residues on epidermal growth factor-like (EGF) repeats of Notch. Mammals have three Fringes: Lunatic, Manic, and Radical. While Lunatic and Manic Fringe inhibit Notch1 activation from Jagged1 and enhance activation from Delta-like 1 (see Drosophila Delta), Radical Fringe enhances signaling from both. A mass spectrometry approach was used to determine whether the variable effects of Fringes on Notch1 result from generation of unique glycosylation patterns on Notch1. Lunatic and Manic Fringe were found to modify similar sites on Notch1, while Radical Fringe modified a subset. Fringe modifications at EGF8 and EGF12 enhanced Notch1 binding to and activation from Delta-like 1, while modifications at EGF6 and EGF36 (added by Manic and Lunatic but not Radical) inhibited Notch1 activation from Jagged1. Combined, these results suggest that Fringe modifications 'mark' different regions in the Notch1 extracellular domain for activation or inhibition.

Monday, March 6th

Cao, W. and Edery, I. (2017). Mid-day siesta in natural populations of D. melanogaster from Africa exhibits an altitudinal cline and is regulated by splicing of a thermosensitive intron in the period clock gene. BMC Evol Biol 17(1): 32. PubMed ID: 28114910
Many diurnal animals exhibit a mid-day 'siesta', generally thought to be an adaptive response aimed at minimizing exposure to heat on warm days, suggesting that in regions with cooler climates mid-day siestas might be a less prominent feature of animal behavior. Drosophila exhibits thermal plasticity in its mid-day siesta that is partly governed by the thermosensitive splicing of the 3'-terminal intron (termed dmpi8) from the key circadian clock gene period (per). For example, decreases in temperature lead to progressively more efficient splicing, which increasingly favors activity over sleep during the mid-day. This study sought to determine if the adaptation of Drosophila from its ancestral range in the lowlands of tropical Africa to the cooler temperatures found at high altitudes involved changes in mid-day sleep behavior and/or dmpi8 splicing efficiency. Using natural populations of Drosophila from different altitudes in tropical Africa, flies from high elevations were shown to have a reduced mid-day siesta and less consolidated sleep. A single nucleotide polymorphism (SNP) in the per 3' UTR has strong effects on dmpi8 splicing and mid-day sleep levels in both low and high altitude flies. Intriguingly, high altitude flies with a particular variant of this SNP exhibit increased dmpi8 splicing efficiency compared to their low altitude counterparts, consistent with reduced mid-day siesta. Thus, a boost in dmpi8 splicing efficiency appears to have played a prominent but not universal role in how African flies adapted to the cooler temperatures at high altitude. These findings point towards mid-day sleep behavior as a key evolutionary target in the thermal adaptation of animals.
Kyriacou, C. P., Green, E. W., Piffer, A. and Dowse, H. B. (2017). Failure to reproduce period-dependent song cycles in Drosophila is due to poor automated pulse-detection and low-intensity courtship. Proc Natl Acad Sci U S A. PubMed ID: 28174268
Stern, 2014 (BMC Biol 12:38) has criticized a body of work from several groups that have independently studied the so-called "Kyriacou and Hall" courtship song rhythms of male Drosophila melanogaster, claiming that these ultradian approximately 60-s cycles in the interpulse interval (IPI) are statistical artifacts that are not modulated by mutations at the period (per) locus. This study has scrutinized Stern's raw data and observed that his automated song pulse-detection method identifies only approximately 50% of the IPIs found by manual (visual and acoustic) monitoring. This critical error is further compounded by Stern's use of recordings with very little song, the large majority of which do not meet the minimal song intensity criteria which Kyriacou and Hall used in their studies. Consequently most of Stern's recordings only contribute noise to the analyses. Of the data presented by Stern, only perL and a small fraction of wild-type males sing vigorously, so this study limited reanalyses to these genotypes. Stern's raw song recordings were manually reexamined, and IPI rhythms were analyzed using several independent time-series analyses. It was observed that perL songs show significantly longer song periods than wild-type songs, with values for both genotypes close to those found in previous studies. These per-dependent differences disappear when the song data are randomized. It is conclude that Stern's negative findings are artifacts of his inadequate pulse-detection methodology coupled to his use of low-intensity courtship song records.
Schwarz, O., Bohra, A. A., Liu, X., Reichert, H., VijayRaghavan, K. and Pielage, J. (2017). Motor control of Drosophila feeding behavior. Elife 6 [Epub ahead of print]. PubMed ID: 28211791
The precise coordination of body parts is essential for survival and behavior of higher organisms. While progress has been made towards the identification of central mechanisms coordinating limb movement, only limited knowledge exists regarding the generation and execution of sequential motor action patterns at the level of individual motoneurons. This study used Drosophila proboscis extension as a model system for a reaching-like behavior. A neuroanatomical description is provided of the motoneurons and muscles contributing to proboscis motion. Using genetic targeting in combination with artificial activation and silencing assays, the individual motoneurons controlling the five major sequential steps of proboscis extension and retraction were identified. Activity-manipulations during naturally evoked proboscis extension show that orchestration of serial motoneuron activation does not rely on feed-forward mechanisms. The data support a model in which central command circuits recruit individual motoneurons to generate task-specific proboscis extension sequences.
Diana, G., Patel, D. S., Entchev, E. V., Zhan, M., Lu, H. and Ch'ng, Q. (2017). Genetic control of encoding strategy in a food-sensing neural circuit. Elife 6. PubMed ID: 28166866
Evolutionary Homolog Study
Neuroendocrine circuits encode environmental information via changes in gene expression and other biochemical activities to regulate physiological responses. Previous work has shown that daf-7 TGFbeta and tph-1 tryptophan hydroxylase expression in specific neurons encode food abundance to modulate lifespan in Caenorhabditis elegans, and uncovered cross- and self-regulation among these genes. This study extends these findings by showing that these interactions between daf-7 and tph-1 regulate redundancy and synergy among neurons in food encoding through coordinated control of circuit-level signal and noise properties. This analysis further shows that daf-7 and tph-1 contribute to most of the food-responsiveness in the modulation of lifespan. A computational model was applied to capture the general coding features of this system. This model agrees with a previous genetic analysis and highlights the consequences of redundancy and synergy during information transmission, suggesting a rationale for the regulation of these information processing features.

Sunday, March 5th

Lee, S., Bao, H., Ishikawa, Z., Wang, W. and Lim, H. Y. (2017). Cardiomyocyte regulation of systemic lipid metabolism by the Apolipoprotein B-containing lipoproteins in Drosophila. PLoS Genet 13(1): e1006555. PubMed ID: 28095410
The heart has emerged as an important organ in the regulation of systemic lipid homeostasis; however, the underlying mechanism remains poorly understood. Drosophila cardiomyocytes regulate systemic lipid metabolism by producing apolipoprotein B-containing lipoproteins (apoB-lipoproteins), essential lipid carriers that are so far known to be generated only in the fat body. In a genetic screen, this study discovered that when haplo-insufficient, microsomal triglyceride transfer protein (mtp), required for the biosynthesis of apoB-lipoproteins, suppressed the development of diet-induced obesity. Tissue-specific inhibition of Mtp revealed that whereas knockdown of mtp only in the fat body decreases systemic triglyceride (TG) content on normal food diet (NFD) as expected, knockdown of mtp only in the cardiomyocytes also equally decreases systemic TG content on NFD, suggesting that the cardiomyocyte- and fat body-derived apoB-lipoproteins serve similarly important roles in regulating whole-body lipid metabolism. Unexpectedly, on high fat diet (HFD), knockdown of mtp in the cardiomyocytes, but not in fat body, protects against the gain in systemic TG levels. It was further shown that inhibition of the Drosophila apoB homologue, apolipophorin or apoLpp, another gene essential for apoB-lipoprotein biosynthesis, affects systemic TG levels similarly to that of Mtp inhibition in the cardiomyocytes on NFD or HFD. Finally, it was determined that HFD differentially alters Mtp and apoLpp expression in the cardiomyocytes versus the fat body, culminating in higher Mtp and apoLpp levels in the cardiomyocytes than in fat body and possibly underlying the predominant role of cardiomyocyte-derived apoB-lipoproteins in lipid metabolic regulation. These findings reveal a novel and significant function of heart-mediated apoB-lipoproteins in controlling lipid homeostasis.
Li, H., Chawla, G., Hurlburt, A.J., Sterrett, M.C., Zaslaver, O., Cox, J., Karty, J.A., Rosebrock, A.P., Caudy, A.A. and Tennessen, J.M. (2017). Drosophila larvae synthesize the putative oncometabolite L-2-hydroxyglutarate during normal developmental growth. Proc Natl Acad Sci U S A 114: 1353-1358. PubMed ID: 28115720
L-2-hydroxyglutarate (L-2HG) has emerged as a putative oncometabolite that is capable of inhibiting enzymes involved in metabolism, chromatin modification, and cell differentiation. However, despite the ability of L-2HG to interfere with a broad range of cellular processes, this molecule is often characterized as a metabolic waste product. This study demonstrates that Drosophila larvae use the metabolic conditions established by aerobic glycolysis to both synthesize and accumulate high concentrations of L-2HG during normal developmental growth. A majority of the larval L-2HG pool is derived from glucose and dependent on the Drosophila estrogen-related receptor (dERR), which promotes L-2HG synthesis by up-regulating expression of the Drosophila homolog of lactate dehydrogenase (dLdh). dLDH is both necessary and sufficient for directly synthesizing L-2HG and the Drosophila homolog of L-2-hydroxyglutarate dehydrogenase (dL2HGDH), which encodes the enzyme that breaks down L-2HG, is required for stage-specific degradation of the L-2HG pool. In addition, dLDH also indirectly promotes L-2HG accumulation via synthesis of lactate, which activates a metabolic feed-forward mechanism that inhibits dL2HGDH activity and stabilizes L-2HG levels. Finally, dLDH and L-2HG influence position effect variegation and DNA methylation, suggesting that this compound serves to coordinate glycolytic flux with epigenetic modifications. Overall, these data demonstrate that growing animal tissues synthesize L-2HG in a controlled manner, reveal a mechanism that coordinates glucose catabolism with L-2HG synthesis, and establish the fly as a unique model system for studying the endogenous functions of L-2HG during cell growth and proliferation.

D'Silva, N. M., Donini, A. and O'Donnell, M. J. (2017). The roles of V-type H+-ATPase and Na+/K+-ATPase in energizing K+ and H+ transport in larval Drosophila gut epithelia. J Insect Physiol [Epub ahead of print]. PubMed ID: 28188726
This study analyzed V- type H+-ATPase (VA) and Na+/K+-ATPase (NKA) along the caeca and midgut of third instar Drosophila larvae using immunohistochemistry and ATPase activity assays. Corresponding H+ and K+ fluxes were characterized using the Scanning Ion-Selective Electrode Technique (SIET), and the roles of transport ATPases in energizing ion transport across the larval gut were investigated by basal application of bafilomycin, a VA inhibitor, and ouabain, a NKA inhibitor. Addition of bafilomycin led to a decrease in H+ absorption along the caeca and midgut except at the copper cells and large flat cell zone of the middle midgut. H+ absorption was decreased by acetazolamide, consistent with carbonic anhydrase activity in all regions except at the large flat cell zone of the middle midgut. Bafilomycin or acetazolamide also led to decreased K+ absorption across the caeca and the anterior midgut. The data show the dependence of K+ transport on H+ gradients established by the VA in the latter regions, consistent with the presence of a Cation-Proton Antiporter (CPA2) identified in other insect epithelia. Addition of ouabain led to the increase of K+ absorption along the anterior midgut and the large flat cell zone of the middle midgut, suggesting a role for the NKA in these regions. This study shows the importance of both ATPases in driving ion transport across the gut of larval Drosophila.
Hsu, H. J. and Drummond-Barbosa, D. (2017). A visual screen for diet-regulated proteins in the Drosophila ovary using GFP protein trap lines. Gene Expr Patterns 23-24: 13-21. PubMed ID: 28093350
The effect of diet on reproduction is well documented in a large number of organisms; however, much remains to be learned about the molecular mechanisms underlying this connection. The Drosophila ovary has a well described, fast and largely reversible response to diet. Ovarian stem cells and their progeny proliferate and grow faster on a yeast-rich diet than on a yeast-free (poor) diet, and death of early germline cysts, degeneration of early vitellogenic follicles and partial block in ovulation further contribute to the approximately 60-fold decrease in egg laying observed on a poor diet. Multiple diet-dependent factors, including insulin-like peptides, the steroid ecdysone, the nutrient sensor Target of Rapamycin, AMP-dependent kinase, and adipocyte factors mediate this complex response. This describe the results of a visual screen using a collection of green fluorescent protein (GFP) protein trap lines to identify additional factors potentially involved in this response. In each GFP protein trap line, an artificial GFP exon is fused in frame to an endogenous protein, such that the GFP fusion pattern parallels the levels and subcellular localization of the corresponding native protein. Fifty-three GFP-tagged proteins were identified that exhibit changes in levels and/or subcellular localization in the ovary at 12-16 hours after switching females from rich to poor diets, suggesting them as potential candidates for future functional studies.

Saturday, March 4th

Tavignot, R., Chaduli, D., Djitte, F., Charroux, B. and Royet, J. (2017). Inhibition of a NF-κB/Diap1 pathway by PGRP-LF is required for proper apoptosis during Drosophila development. PLoS Genet [Epub ahead of print]. PubMed ID: 28085885
NF-κB pathways are key signaling cascades of the Drosophila innate immune response. One of them, the Immune Deficiency (IMD) pathway, is under a very tight negative control. Although molecular brakes exist at each step of this signaling module from ligand availability to transcriptional regulation, it remains unknown whether repressors act in the same cells or tissues and if not, what is rationale behind this spatial specificity. This study shows that the negative regulator of IMD pathway PGRP-LF is epressed in ectodermal derivatives. In the absence of any immune elicitor, PGRP-LF loss-of-function mutants display a constitutive NF-κB/IMD activation specifically in ectodermal tissues leading to genitalia and tergite malformations. In agreement with previous data showing that proper development of these structures requires induction of apoptosis, it was found that ectopic activation of NF-κB/IMD signaling leads to apoptosis inhibition in both genitalia and tergite primordia. NF-κB/IMD signaling antagonizes apoptosis by up-regulating expression of the anti-apoptotic protein Diap1. Altogether these results show that, in the complete absence of infection, the negative regulation of NF-κB/IMD pathway by PGRP-LF is crucial to ensure proper induction of apoptosis and consequently normal fly development. These results highlight that IMD pathway regulation is controlled independently in different tissues, probably reflecting the different roles of this signaling cascade in both developmental and immune processes.

Howick, V. M. and Lazzaro, B. P. (2017). The genetic architecture of defense as resistance to and tolerance of bacterial infection in Drosophila melanogaster. Mol Ecol [Epub ahead of print]. PubMed ID: 28099780
Defense against pathogenic infection can take two forms: resistance and tolerance. Resistance is the ability of the host to limit a pathogen burden, whereas tolerance is the ability to limit the negative consequences of infection at a given level of infection intensity. Evolutionarily, a tolerance strategy that is independent of resistance could allow the host to avoid mounting a costly immune response and, theoretically, to avoid a coevolutionary arms race between pathogen virulence and host resistance. In order to understand the impact of tolerance on host defense and identify genetic variants that determine host tolerance, genetic variation in tolerance was defined as the residual deviation from a binomial regression of fitness under infection against infection intensity. A genome-wide association study (GWAS) was performed to map the genetic basis of variation in resistance to and tolerance of infection by the bacterium Providencia rettgeri. Positive genetic correlation was found between resistance and tolerance, and the level of resistance was highly predictive of tolerance. Thirty loci were identified that predict tolerance, many of which are in genes involved in the regulation of immunity and metabolism. RNAi was performed to confirm that a subset of mapped genes have a role in defense, including putative wound repair genes grainy head and debris buster. The results indicate that tolerance is not an independent strategy from resistance, but that defense arises from a collection of physiological processes intertwined with canonical immunity and resistance.
White, P. M., Pietri, J. E., Debec, A., Russell, S., Patel, B. and Sullivan, W. (2017). Mechanisms of horizontal cell-to-cell transfer of Wolbachia spp. in Drosophila melanogaster. Appl Environ Microbiol [Epub ahead of print]. PubMed ID: 28087534
Several studies indicate that Wolbachia is capable of transfer between somatic and germline cells during nematode development and in adult flies. However, the mechanisms underlying horizontal cell-to-cell transfer remain largely unexplored. This study establish a tractable system for probing horizontal transfer of Wolbachia between Drosophila cells in culture using fluorescence in situ hybridization (FISH). First, it was shown that horizontal transfer is independent of cell-to-cell contact and can efficiently take place through the culture medium within hours. Further, it was demonstrate that efficient transfer utilizes host cell phagocytic and clathrin/dynamin-dependent endocytic machinery. Lastly, evidence is provided that this process is conserved between species, showing that horizontal transfer from mosquito to Drosophila cells takes place in a similar fashion. Taken together, these results indicate that Wolbachia utilize host internalization machinery during infection, and this mechanism is conserved across insect species.
Surendran, S., Huckesfeld, S., Waschle, B. and Pankratz, M. J. (2017). Pathogen induced food evasion behavior in Drosophila larvae. J Exp Biol. PubMed ID: 28254879
Recognizing a deadly pathogen and generating an appropriate immune reaction is essential for any organism to survive in its natural habitat. Unlike vertebrates and higher primates, invertebrates depend solely on the innate immune system to defend themselves from an attacking pathogen. This paper reports a behavioral defense strategy observed in Drosophila larvae that help them escape and limit an otherwise lethal infection. A bacterial infection in the gut is sensed by the larval central nervous system which generates an alteration in its food preference, leading them to stop feeding and move away from the infectious food source. This behavioral response is dependent on the internal nutritive state of the larvae. Using this novel behavioral assay as a read-out, hugin neuropeptide to be involved in evasion response and detection of bacterial signals.

Friday, March 3rd

Zhang, J., Liu, Y., Jiang, K. and Jia, J. (2017). SUMO regulates the activity of Smoothened and Costal-2 in Drosophila Hedgehog signaling. Sci Rep 7: 42749. PubMed ID: 28195188
In Hedgehog (Hh) signaling, the GPCR-family protein Smoothened (Smo) acts as a signal transducer that is regulated by phosphorylation and ubiquitination, which ultimately change the cell surface accumulation of Smo. However, it is not clear whether Smo is regulated by other post-translational modifications, such as sumoylation. This study demonstrates that knockdown of the small ubiquitin-related modifier (SUMO) pathway components Ubc9 (a SUMO-conjugating enzyme E2), PIAS (a SUMO-protein ligase E3), and Smt3 (the SUMO isoform in Drosophila) by RNAi prevents Smo accumulation and alters Smo activity in the wing. Hh-induced-sumoylation stabilizes Smo, whereas desumoylation by Ulp1 destabilizes Smo in a phosphorylation independent manner. Mechanistically, excessive Krz, the Drosophila β-arrestin 2, inhibits Smo sumoylation and prevents Smo accumulation through Krz regulatory domain. Krz likely facilitates the interaction between Smo and Ulp1 because knockdown of Krz by RNAi attenuates Smo-Ulp1 interaction. Finally, Cos2 is also sumoylated, which counteracts its inhibitory role on Smo accumulation in the wing. Taken together, these results uncover a novel mechanism for Smo activation by sumoylation that is regulated by Hh and Smo interacting proteins.
Martins, T., Eusebio, N., Correia, A., Marinho, J., Casares, F. and Pereira, P. S. (2017). TGFβ/Activin signalling is required for ribosome biogenesis and cell growth in Drosophila salivary glands. Open Biol 7(1). PubMed ID: 28123053
Signalling by TGFβ superfamily factors plays an important role in tissue growth and cell proliferation. In Drosophila, the activity of the TGFβ/Activin signalling branch has been linked to the regulation of cell growth and proliferation, but the cellular and molecular basis for these functions are not fully understood. This study shows that both the RII receptor Punt (Put) and the R-Smad Smad2 are strongly required for cell and tissue growth. Knocking down the expression of Put or Smad2 in salivary glands causes alterations in nucleolar structure and functions. Cells with decreased TGFβ/Activin signalling accumulate intermediate pre-rRNA transcripts containing internal transcribed spacer 1 regions accompanied by the nucleolar retention of ribosomal proteins. Thus, these results show that TGFβ/Activin signalling is required for ribosomal biogenesis, a key aspect of cellular growth control. Importantly, overexpression of Put enhanced cell growth induced by Drosophila Myc, a well-characterized inducer of nucleolar hypertrophy and ribosome biogenesis.
Lu, T.Y., MacDonald, J.M., Neukomm, L.J., Sheehan, A.E., Bradshaw, R., Logan, M.A. and Freeman, M.R. (2017). Axon degeneration induces glial responses through Draper-TRAF4-JNK signalling. Nat Commun 8: 14355. PubMed ID: 28165006
Draper/Ced-1/MEGF-10 is an engulfment receptor that promotes clearance of cellular debris in C. elegans, Drosophila and mammals. Draper signals through an evolutionarily conserved Src family kinase cascade to drive cytoskeletal rearrangements and target engulfment through Rac1. Glia also alter gene expression patterns in response to axonal injury but pathways mediating these responses are poorly defined. This study shows that Draper is cell autonomously required for glial activation of transcriptional reporters after axonal injury. The TNF receptor associated factor 4 (TRAF4) was identified as a novel Draper binding partner that is required for reporter activation and phagocytosis of axonal debris. TRAF4 and misshapen (MSN) act downstream of Draper to activate c-Jun N-terminal kinase (JNK) signalling in glia, resulting in changes in transcriptional reporters that are dependent on Drosophila AP-1 (dAP-1) and STAT92E. These data argue injury signals received by Draper at the membrane are important regulators of downstream transcriptional responses in reactive glia.

Ma, X., Wang, H., Ji, J., Xu, W., Sun, Y., Li, W., Zhang, X., Chen, J. and Xue, L. (2017). Hippo signaling promotes JNK-dependent cell migration. Proc Natl Acad Sci U S A [Epub ahead of print]. PubMed ID: 28174264
Overwhelming studies show that dysregulation of the Hippo pathway is positively correlated with cell proliferation, growth, and tumorigenesis. Paradoxically, the detailed molecular roles of the Hippo pathway in cell invasion remain debatable. Using a Drosophila invasion model in wing epithelium, this study shows that activated Hippo signaling promotes cell invasion and epithelial-mesenchymal transition through JNK, as inhibition of JNK signaling dramatically blocks Hippo pathway activation-induced matrix metalloproteinase 1 expression and cell invasion. Furthermore, bantam-Rox8 modules act as essential components downstream of Yorkie in mediating JNK-dependent cell invasion. Finally, YAP (Yes-associated protein) expression negatively regulates TIA1 (Rox8 ortholog) expression and cell invasion in human cancer cells. Together, these findings provide molecular insights into Hippo pathway-mediated cell invasion and also raise a noteworthy concern in therapeutic interventions of Hippo-related cancers, as simply inhibiting Yorkie or YAP activity might paradoxically accelerate cell invasion and metastasis.

Thursday, March 2nd

Hashimoto, Y., Takahashi, M., Sakota, E. and Nakamura, Y. (2017). Nonstop-mRNA decay machinery is involved in the clearance of mRNA 5'-fragments produced by RNAi and NMD in Drosophila melanogaster cells. Biochem Biophys Res Commun 484(1): 1-7. PubMed ID: 28115162
When translating mRNAs are cleaved in protein-coding regions, 5' fragments of mRNAs are detached from stop codons (i.e., nonstop mRNAs) and protected from 3'-5' exonucleases by ribosomes stalled at the 3' termini. It has been shown in yeast that the nonstop mRNA decay (NSD) machinery triggers nonstop mRNA degradation by removing stalled ribosomes in the artificial reporter mRNAs. However, it is not known well whether NSD is involved in the degradation of endogenous nonstop mRNAs in higher eukaryotes. The question of whether 5'-nonstop-mRNA fragments generated by siRNA cleavage or nonsense-mediated-mRNA decay (NMD) are degraded by the NSD pathway in was addressed Drosophila melanogaster cells by knocking down three NSD components, Pelota (a yeast Dom34 homolog), Hbs1 and ABCE1 (a ribosome-recycling factor). Double, but not single, knockdown of any two of these three factors efficiently stabilized nonstop reporter mRNAs and triple knockdown of Pelota, Hbs1 and ABCE1 further stabilized nonstop mRNAs in highly ribosome-associated state. These findings demonstrated that Pelota, Hbs1 and ABCE1 are crucial for NSD in Drosophila cells as in yeast for rescuing stalled ribosomes and degrading nonstop mRNAs. This is the first comprehensive report to show the involvement of the NSD machinery in the clearance of mRNA 5'-fragments produced by RNAi and NMD in eukaryotes.
Shimada, Y., Mohn, F. and Bühler, M. (2016). The RNA-induced transcriptional silencing complex targets chromatin exclusively via interacting with nascent transcripts. Genes Dev 30: 2571-2580. PubMed ID: 27941123
Evolutionary Homolog Study:
Small RNAs regulate chromatin modification and transcriptional gene silencing across the eukaryotic kingdom. Although these processes have been well studied, fundamental mechanistic aspects remain obscure. Specifically, it is unclear exactly how small RNA-loaded Argonaute (see Drosophila Ago1) protein complexes target chromatin to mediate silencing (see Drosophila post-transcriptional gene silencing). Using fission yeast, this study demonstrates that transcription of the target locus is essential for RNA-directed formation of heterochromatin. However, high transcriptional activity is inhibitory; thus, a transcriptional window exists that is optimal for silencing. It was found that pre-mRNA splicing is compatible with RNA-directed heterochromatin formation. However, the kinetics of pre-mRNA processing is critical. Introns close to the 5' end of a transcript that are rapidly spliced result in a bistable response whereby the target either remains euchromatic or becomes fully silenced. Together, these results discount siRNA-DNA base pairing in RNA-mediated heterochromatin formation, and the mechanistic insights further reveal guiding paradigms for the design of small RNA-directed chromatin silencing studies in multicellular organisms.

Sgromo, A., Raisch, T., Bawankar, P., Bhandari, D., Chen, Y., Kuzuoğlu-Öztürk, D., Weichenrieder, O. and Izaurralde, E. (2017). A CAF40-binding motif facilitates recruitment of the CCR4-NOT complex to mRNAs targeted by Drosophila Roquin. Nat Commun 8: 14307. PubMed ID: 28165457
Human (Hs) Roquin1 and Roquin2 are RNA-binding proteins that promote mRNA target degradation through the recruitment of the CCR4-NOT deadenylase complex and are implicated in the prevention of autoimmunity. Roquin1 recruits CCR4-NOT via a C-terminal region that is not conserved in Roquin2 or in invertebrate Roquin. This study shows that Roquin2 and Drosophila melanogaster (Dm) Roquin also interact with the CCR4-NOT complex through their C-terminal regions. The C-terminal region of Dm Roquin contains multiple motifs that mediate CCR4-NOT binding. One motif binds to the CAF40 subunit of the CCR4-NOT complex. The crystal structure of the Dm Roquin CAF40-binding motif (CBM) bound to CAF40 reveals that the CBM adopts an α-helical conformation upon binding to a conserved surface of CAF40. Thus, despite the lack of sequence conservation, the C-terminal regions of Roquin proteins act as an effector domain that represses the expression of mRNA targets via recruitment of the CCR4-NOT complex.

Chinen, M. and Lei, E. P. (2017). Drosophila Argonaute2 turnover is regulated by the ubiquitin proteasome pathway. Biochem Biophys Res Commun [Epub ahead of print]. PubMed ID: 28087276
Argonaute (AGO) proteins play a central role in the RNA interference (RNAi) pathway, which is a cytoplasmic mechanism important for post-transcriptional regulation of gene expression. In Drosophila, AGO2 also functions in the nucleus to regulate chromatin insulator activity and transcription. Although there are a number of studies focused on AGO2 function, the regulation of AGO2 turnover is not well understood. This study found that mutation of T1149 or R1158 in the conserved PIWI domain causes AGO2 protein instability, but only T1149 affects RNAi activity. Mass spec analysis shows that several proteasome components co-purify with both wildtype and mutant AGO2, and knockdown of two proteasome pathway components results in AGO2 protein accumulation. Finally, AGO2 protein levels increase after treatment with the proteasome inhibitor MG132. These results indicate that the ubiquitin-proteasome pathway is involved in AGO2 protein turnover.

Wednesday, March 1st

Kuntz, S., Poeck, B. and Strauss, R. (2017). Visual working memory requires permissive and instructive NO/cGMP signaling at presynapses in the Drosophila central brain. Curr Biol [Epub ahead of print]. PubMed ID: 28216314
The gaseous second messenger nitric oxide (NO) has been shown to regulate memory formation by activating retrograde signaling cascades from post- to presynapse that involve cyclic guanosine monophosphate (cGMP) production to induce synaptic plasticity and transcriptional changes. This study analyzed the role of NO in the formation of a visual working memory that lasts only a few seconds. This memory is encoded in a subset of ring neurons that form the ellipsoid body in the Drosophila brain. Using genetic and pharmacological manipulations, NO signaling was shown to be required for cGMP-mediated CREB activation, leading to the expression of competence factors like the synaptic homer protein. Interestingly, this cell-autonomous function can also be fulfilled by hydrogen sulfide (H2S) through a converging pathway, revealing for the first time that endogenously produced H2S has a role in memory processes. Notably, the NO synthase is strictly localized to the axonal output branches of the ring neurons, and this localization seems to be necessary for a second, phasic role of NO signaling. Evidence is provided for a model where NO modulates the opening of cGMP-regulated cation channels to encode a short-term memory trace. Local production of NO/cGMP in restricted branches of ring neurons seems to represent the engram for objects, and comparing signal levels between individual ring neurons is used to orient the fly during search behavior. Due to its short half-life, NO seems to be a uniquely suited second messenger to encode working memories that have to be restricted in their duration.
Keles, M. F. and Frye, M. A. (2017). Object-detecting neurons in Drosophila. Curr Biol [Epub ahead of print]. PubMed ID: 28190726
Many animals rely on vision to detect objects such as conspecifics, predators, and prey. Hypercomplex cells found in feline cortex and small target motion detectors found in dragonfly and hoverfly optic lobes demonstrate robust tuning for small objects, with weak or no response to larger objects or movement of the visual panorama. However, the relationship among anatomical, molecular, and functional properties of object detection circuitry is not understood. This study characterized a specialized object detector in Drosophila, the lobula columnar neuron LC11. By imaging calcium dynamics with two-photon excitation microscopy, it was shown that LC11 responds to the omni-directional movement of a small object darker than the background, with little or no responses to static flicker, vertically elongated bars, or panoramic gratings. LC11 dendrites innervate multiple layers of the lobula, and each dendrite spans enough columns to sample 75 degrees of visual space, yet the area that evokes calcium responses is only 20 degrees wide and shows robust responses to a 2.2 degrees object spanning less than half of one facet of the compound eye. The dendrites of neighboring LC11s encode object motion retinotopically, but the axon terminals fuse into a glomerular structure in the central brain where retinotopy is lost. Blocking inhibitory ionic currents abolishes small object sensitivity and facilitates responses to elongated bars and gratings. These results reveal high-acuity object motion detection in the Drosophila optic lobe.
Lindsay, T., Sustar, A. and Dickinson, M. (2017). The Function and Organization of the Motor System Controlling Flight Maneuvers in Flies. Curr Biol 27(3): 345-358. PubMed ID: 28132816
Animals face the daunting task of controlling their limbs using a small set of highly constrained actuators. This problem is particularly demanding for insects such as Drosophila, which must adjust wing motion for both quick voluntary maneuvers and slow compensatory reflexes using only a dozen pairs of muscles. To identify strategies by which animals execute precise actions using sparse motor networks, the activity was imagined of a complete ensemble of wing control muscles in intact, flying flies. The experiments uncovered a remarkably efficient logic in which each of the four skeletal elements at the base of the wing are equipped with both large phasically active muscles capable of executing large changes and smaller tonically active muscles specialized for continuous fine-scaled adjustments. Based on the responses to a broad panel of visual motion stimuli, a model is developed by which the motor array regulates aerodynamically functional features of wing motion.
Schwarz, S., Mangan, M., Zeil, J., Webb, B. and Wystrach, A. (2017). How Ants Use Vision When Homing Backward. Curr Biol 27(3): 401-407. PubMed ID: 28111152
Evolutionary Homolog Study
Ants can navigate over long distances between their nest and food sites using visual cues. Can ants use their visual memories of the terrestrial cues when going backward? The results suggest that ants do not adjust their direction of travel based on the perceived scene while going backward. Instead, they maintain a straight direction using their celestial compass. This direction can be dictated by their path integrator but can also be set using terrestrial visual cues after a forward peek. If the food item is too heavy to enable body rotations, ants moving backward drop their food on occasion, rotate and walk a few steps forward, return to the food, and drag it backward in a now-corrected direction defined by terrestrial cues. Furthermore, it was shown that ants can maintain their direction of travel independently of their body orientation. It thus appears that egocentric retinal alignment is required for visual scene recognition, but ants can translate this acquired directional information into a holonomic frame of reference, which enables them to decouple their travel direction from their body orientation and hence navigate backward. This reveals substantial flexibility and communication between different types of navigational information: from terrestrial to celestial cues and from egocentric to holonomic directional memories.
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