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

Sunday, November 15th

Kwong, P. N., Chambers, M., Vashisht, A. A., Turki-Judeh, W., Yau, T. Y., Wohlschlegel, J. A. and Courey, A. J. (2015). The central region of the Drosophila co-repressor Groucho as a regulatory hub. J Biol Chem [Epub ahead of print]. PubMed ID: 26483546 Summary: Groucho (Gro) is a Drosophila co-repressor that regulates the expression of a large number of genes, many of which are involved in developmental control. This study has identified multiple embryonic Gro-interacting proteins. The interactors include protein complexes involved in chromosome organization, mRNA processing, and signaling. Further investigation of the interacting proteins using a reporter assay showed that many of them modulate Gro-mediated repression either positively or negatively. The positive regulators include components of the spliceosomal subcomplex U1 small nuclear ribonucleoprotein (U1 snRNP). A co-immunoprecipitation experiment confirms this finding and suggests that a sizable fraction of nuclear U1 snRNP is associated with Gro. The use of RNA-seq to analyze the gene expression profile of cells subjected to knockdown of Gro or snRNP-U1-C (a component of U1 snRNP) showed a significant overlap between genes regulated by these two factors. Furthermore, comparison of our RNA-seq data to Gro and Pol II ChIP data led to a number of insights including the finding that Gro-repressed genes are enriched for promoter proximal Pol II. It is concluded that the Gro central domains mediate multiple interactions required for repression thus functioning as a regulatory hub. Furthermore, interactions with the spliceosome may contribute to repression by Gro.

Hardie, R. C., Liu, C. H., Randall, A. S. and Sengupta, S. (2015). In vivo tracking of phosphoinositides in Drosophila photoreceptors. J Cell Sci [Epub ahead of print]. PubMed ID: 26483384 Summary: In order to monitor phosphoinositide turnover during phospholipase C (PLC) mediated Drosophila phototransduction, fluorescently tagged lipid probes were expressed in photoreceptors and imaged both in dissociated cells, and in eyes of intact living flies. Of six probes tested, TbR332H (mutant of the Tubby protein pleckstrin homology domain) was judged the best reporter for PtdIns(4,5)P2, and the P4M domain from Legionella SidM for PtdIns4P. Using accurately calibrated illumination, these indicated that only approximately 50% of PtdIns(4,5)P2 and very little PtdIns4P were depleted by full daylight intensities in wild-type flies, but both were severely depleted by approximately 100-fold dimmer intensities in mutants lacking Ca2+ permeable TRP channels or protein kinase C (PKC). Resynthesis of PtdIns4P (t(1/2) approximately 12 s) was faster than PtdIns(4,5)P2 (t(1/2) approximately 40s), but both were greatly slowed in mutants of DAG kinase (rdgA) or PtdIns transfer protein (rdgB). The results indicate that Ca2+ and PKC-dependent inhibition of PLC is critical for enabling photoreceptors to maintain phosphoinositide levels despite high rates of hydrolysis by PLC, and suggest phosphorylation of PtdIns4P to PtdIns(4,5)P2 is the rate-limiting step of the cycle.

Choo, A., O'Keefe, L. V., Lee, C. S., Gregory, S. L., Shaukat, Z., Colella, A., Lee, K., Denton, D. and Richards, R. I. (2015). Tumor suppressor WWOX moderates the mitochondrial respiratory complex. Genes Chromosomes Cancer. PubMed ID: 26390919 Summary: Fragile site FRA16D exhibits DNA instability in cancer, resulting in diminished levels of protein from the WWOX gene that spans it. WWOX suppresses tumor growth by an undefined mechanism. WWOX participates in pathways involving aerobic metabolism and reactive oxygen species. WWOX comprises two WW domains as well as a short-chain dehydrogenase/reductase enzyme. This study describes an in vivo genetic analysis in Drosophila melanogaster to identify functional interactions between WWOX and metabolic pathways. Altered WWOX levels modulate variable cellular outgrowths caused by genetic deficiencies of components of the mitochondrial respiratory complexes. This modulation requires the enzyme active site of WWOX, and the defective respiratory complex-induced cellular outgrowths are mediated by reactive oxygen species, dependent upon the Akt pathway and sensitive to levels of autophagy and hypoxia-inducible factor. WWOX is known to contribute to homeostasis by regulating the balance between oxidative phosphorylation and glycolysis. Reduction of WWOX levels results in diminished ability to respond to metabolic perturbation of normal cell growth. Thus, the ability of WWOX to facilitate escape from mitochondrial damage-induced glycolysis (Warburg effect) is, therefore, a plausible mechanism for its tumor suppressor activity.

Khire, A., Vizuet, A. A., Davila, E. and Avidor-Reiss, T. (2015). Asterless reduction during spermiogenesis is regulated by Plk4 and is essential for zygote development in Drosophila. Curr Biol [Epub ahead of print]. PubMed ID: 26480844 Summary: Centrosome reduction is the decrease in centrosomal components during spermatid differentiation (spermiogenesis). It is one of several dramatic subcellular reorganizations that lead to spermatozoa formation common to a wide range of animals. However, the mechanism underlying centrosome reduction is unknown and its functions are unclear. This study shows that in Drosophila melanogaster spermiogenesis, the quantity of centrosomal proteins is dramatically reduced; for example, Asterless (Asl) is reduced approximately 500-fold and is barely detected in spermatozoa. Asl reduction is regulated through a subset of its domains by the master regulator of centriole duplication Plk4 and by the ubiquitin ligase that targets Plk4 for degradation: Slimb. When Asl reduction is attenuated by Asl overexpression, plk4 mutations, Plk4 RNAi, or Slimb overexpression, Asl levels are higher in spermatozoa, resulting in embryos with reduced viability. Significantly, overexpressing Plk4 and Asl simultaneously, or combining plk4 and slimb mutations, balances their opposing effects on Asl reduction, restoring seemingly normal fertility. This suggests that increased Asl levels cause the observed reduced fertility and not other pleotropic effects. Attenuation of Asl reduction also causes delayed development and a failure to form astral microtubules in the zygote. Together, this study provides the first insight into a molecular mechanism that regulates centrosome reduction and the first direct evidence that centrosome reduction is essential for post-fertilization development.

Saturday, November 14th

Mattila, J., Havula, E., Suominen, E., Teesalu, M., Surakka, I., Hynynen, R., Kilpinen, H., Väänänen, J., Hovatta, I., Käkelä, R., Ripatti, S., Sandmann, T. and Hietakangas, V. (2015). Mondo-Mlx mediates organismal sugar sensing through the Gli-similar transcription factor Sugarbabe. Cell Rep [Epub ahead of print]. PubMed ID: 26440885 Summary: The ChREBP/Mondo-Mlx transcription factors are activated by sugars and are essential for sugar tolerance. They promote the conversion of sugars to lipids, but beyond this, their physiological roles are insufficiently understood. This study demonstrates that in an organism-wide setting in Drosophila, Mondo-Mlx controls the majority of sugar-regulated genes involved in nutrient digestion and transport as well as carbohydrate, amino acid, and lipid metabolism. Furthermore, human orthologs of the Mondo-Mlx targets display enrichment among gene variants associated with high circulating triglycerides. In addition to direct regulation of metabolic genes, Mondo-Mlx maintains metabolic homeostasis through downstream effectors, including the Activin ligand Dawdle and the Gli-similar transcription factor Sugarbabe. Sugarbabe controls a subset of Mondo-Mlx-dependent processes, including de novo lipogenesis and fatty acid desaturation. In sum, Mondo-Mlx is a master regulator of other sugar-responsive pathways essential for adaptation to a high-sugar diet.

Marada, S., Truong, A. and Ogden, S. K. (2015). The small GTPase Rap1 is a modulator of Hedgehog signaling. Dev Biol [Epub ahead of print]. PubMed ID: 26481064 Summary: During development, the evolutionarily conserved Hedgehog (Hh) morphogen provides instructional cues that influence cell fate, cell affinity and tissue morphogenesis. To do so, the Hh signaling cascade must coordinate its activity with other morphogenetic signals. This can occur through engagement of or response to effectors that do not typically function as core Hh pathway components. Given the ability of small G proteins of the Ras family to impact cell survival, differentiation, growth and adhesion, it was of interest to determine whether Hh and Ras signaling might intersect during development. Genetic modifier tests were performed in Drosophila to examine the ability of select Ras family members to influence Hh signal output, and Rap1 was identified as a positive modulator of Hh pathway activity. The results suggest that Rap1 is activated to its GTP-bound form in response to Hh ligand, and that the GTPase exchange factor C3G likely contributes to this activation. The Rap1 effector Canoe (Cno) also impacts Hh signal output, suggesting that a C3G-Rap1-Cno axis intersects the Hh pathway during tissue morphogenesis.

Deshpande, S.A., Yamada, R., Mak, C.M., Hunter, B., Soto Obando, A., Hoxha, S. and Ja, W.W. (2015). Acidic food pH increases palatability and consumption and extends Drosophila lifespan. J Nutr [Epub ahead of print]. PubMed ID: 26491123 Summary: Despite the prevalent use of Drosophila as a model in studies of nutrition, the effects of fundamental food properties, such as pH, on animal health and behavior are not well known. This study examined the effect of food pH on adult Drosophila lifespan, feeding behavior, and microbiota composition and tested the hypothesis that pH-mediated changes in palatability and total consumption are required for modulating longevity. The effect of buffered food (pH 5, 7, or 9) was measured on male gustatory responses (proboscis extension), total food intake, and male and female lifespan. The effect of food pH on germfree male lifespan was also assessed. Changes in fly-associated microbial composition as a result of food pH were determined by 16S ribosomal RNA gene sequencing. Male gustatory responses, total consumption, and male and female longevity were additionally measured in the taste-defective Pox neuro (Poxn) mutant and its transgenic rescue control. An acidic diet increases Drosophila gustatory responses (40-230%) and food intake (5-50%) and extends survival (10-160% longer median lifespan) compared with flies on either neutral or alkaline pH food. Alkaline food pH shifts the composition of fly-associated bacteria and results in greater lifespan extension (260% longer median survival) after microbes are eliminated compared with flies on an acidic (50%) or neutral (130%) diet. However, germfree flies live longer on an acidic diet (5-20% longer median lifespan) compared with those on either neutral or alkaline pH food. Gustatory responses, total consumption, and longevity are unaffected by food pH in Poxn mutant flies. Food pH can directly influence palatability and feeding behavior and affect parameters such as microbial growth to ultimately affect Drosophila lifespan. Fundamental food properties altered by dietary or drug interventions may therefore contribute to changes in animal physiology, metabolism, and survival.

Camus, M. F., Wolf, J. B., Morrow, E. H. and Dowling, D. K. (2015). Single nucleotides in the mtDNA sequence modify mitochondrial molecular function and are associated with sex-specific effects on fertility and aging. Curr Biol 25: 2717-2722. PubMed ID: 26455309 Summary: Mitochondria underpin energy conversion in eukaryotes. Their small genomes have been the subject of increasing attention, and there is evidence that mitochondrial genetic variation can affect evolutionary trajectories and shape the expression of life-history traits considered to be key human health indicators. However, it is not understood how genetic variation across a diminutive genome, which in most species harbors only about a dozen protein-coding genes, can exert broad-scale effects on the organismal phenotype. Such effects are particularly puzzling given that the mitochondrial genes involved are under strong evolutionary constraint and that mitochondrial gene expression is highly conserved across diverse taxa. This study used replicated genetic lines in the fruit fly, Drosophila melanogaster, each characterized by a distinct and naturally occurring mitochondrial haplotype placed alongside an isogenic nuclear background. Sequence variation within the mitochondrial DNA (mtDNA) affects both the copy number of mitochondrial genomes and patterns of gene expression across key mitochondrial protein-coding genes. In several cases, haplotype-mediated patterns of gene expression were gene-specific, even for genes from within the same transcriptional units. This invokes post-transcriptional processing of RNA in the regulation of mitochondrial genetic effects on organismal phenotypes. Notably, the haplotype-mediated effects on gene expression could be traced backward to the level of individual nucleotides and forward to sex-specific effects on fertility and longevity. This study thus elucidates how small-scale sequence changes in the mitochondrial genome can achieve broad-scale regulation of health-related phenotypes and even contribute to sex-related differences in longevity.

Friday, November 13th

Muhammad, K., et al. (2015). Presynaptic spinophilin tunes neurexin signalling to control active zone architecture and function. Nat Commun 6: 8362. PubMed ID: 26471740 Summary: Assembly and maturation of synapses at the Drosophila neuromuscular junction (NMJ) depend on trans-synaptic neurexin/neuroligin signalling, which is promoted by the scaffolding protein Syd-1 binding to neurexin. This study reports that the scaffold protein spinophilin binds to the C-terminal portion of neurexin and is needed to limit neurexin/neuroligin signalling by acting antagonistic to Syd-1. Loss of presynaptic spinophilin results in the formation of excess, but atypically small active zones. Neuroligin-1/neurexin-1/Syd-1 levels are increased at spinophilin mutant NMJs, and removal of single copies of the neurexin-1, Syd-1 or neuroligin-1 genes suppresses the spinophilin-active zone phenotype. Evoked transmission is strongly reduced at spinophilin terminals, owing to a severely reduced release probability at individual active zones. It is concluded that presynaptic spinophilin fine-tunes neurexin/neuroligin signalling to control active zone number and functionality, thereby optimizing them for action potential-induced exocytosis.

Chen, Z., Chen, H. C. and Montell, C. (2015). TRP and Rhodopsin transport depends on dual XPORT ER chaperones encoded by an operon. Cell Rep 13: 573-584. PubMed ID: 26456832 Summary: TRP channels and G protein-coupled receptors (GPCRs) play critical roles in sensory reception. However, the identities of the chaperones that assist GPCRs in translocating from the endoplasmic reticulum (ER) are limited, and TRP ER chaperones are virtually unknown. The one exception for TRPs is Drosophila XPORT. This study shows that the xport locus is bicistronic and encodes unrelated transmembrane proteins, which enable the signaling proteins that initiate and culminate phototransduction, rhodopsin 1 (Rh1) and TRP, to traffic to the plasma membrane. XPORT-A (CG4468) and XPORT-B are ER proteins, and loss of either has a profound impact on TRP and Rh1 targeting to the light-sensing compartment of photoreceptor cells. XPORT-B complexed in vivo with the Drosophila homolog of the mammalian HSP70 protein, GRP78/BiP (Heat shock 70-kDa protein cognate 3), which, in turn, associated with Rh1. This work highlights a coordinated network of chaperones required for the biosynthesis of the TRP channel and rhodopsin in Drosophila photoreceptor cells.

Hicks, L., Liu, G., Ukken, F. P., Lu, S., Bollinger, K. E., O'Connor-Giles, K. and Gonsalvez, G. B. (2015). Depletion or over-expression of Sh3px1 results in dramatic changes in cell morphology. Biol Open [Epub ahead of print]. PubMed ID: 26459243 Summary: The mammalian Sorting Nexin 9 (Snx9) contains an Sh3 domain at its N-terminus and interacts with Dynamin and actin nucleation factors via this domain. Snx9 also contains a C-terminal BAR domain, known to sense and/or induce membrane curvature. The Snx9 family is encoded by a single gene in Drosophila called sh3px1. This report presents an initial characterization of sh3px1. Depletion of Sh3px1 from Drosophila Schneider 2 (S2) cells resulted in defective lamellipodia formation. A similar phenotype has been reported upon depletion of Scar, the actin nucleation factor implicated in forming lamellipodia. In addition, over-expression of Sh3px1 in S2 cells results in the formation of tubules as well as long protrusions. Formation of these structures required the C-terminal BAR domain as well as the adjacent Phox homology (PX) domain of Sh3px1. Furthermore, efficient protrusion formation by Sh3px1 required the actin nucleation factor Wasp. Tubules and protrusions were also generated upon over-expressing the mammalian orthologs Snx18 and Snx33 in S2 cells. By contrast, over-expressing Snx9 mostly induced long tubules.

Peng, Y., Lee, J., Rowland, K., Wen, Y., Hua, H., Carlson, N., Lavania, S., Parrish, J. Z. and Kim, M. D. (2015). Regulation of dendrite growth and maintenance by exocytosis. J Cell Sci [Epub ahead of print]. PubMed ID: 26483382 Summary: Dendrites lengthen by several orders of magnitude during neuronal development, but how membrane is allocated in dendrites to facilitate this growth remains unclear. This study reports that Ras opposite (Rop), the Drosophila ortholog of the key exocytosis regulator Munc18-1, is an essential factor mediating dendrite growth. Neurons with depleted Rop function exhibit reduced terminal dendrite outgrowth followed by primary dendrite degeneration, suggestive of differential requirements for exocytosis in the growth and maintenance of different dendritic compartments. Rop promotes dendrite growth together with the exocyst, an octameric protein complex involved in tethering vesicles to the plasma membrane, with Rop-exocyst complexes and exocytosis predominating in primary dendrites over terminal dendrites. By contrast, membrane-associated proteins readily diffuse from primary dendrites into terminals, but not in the reverse direction, suggesting that diffusion, rather than targeted exocytosis, supplies membranous material for terminal dendritic growth, revealing key differences in the distribution of materials to these expanding dendritic compartments.

Thursday, November 12th

Dhanyasi, N., Segal, D., Shimoni, E., Shinder, V., Shilo, B.Z., VijayRaghavan, K. and Schejter, E.D. (2015). Surface apposition and multiple cell contacts promote myoblast fusion in Drosophila flight muscles. J Cell Biol 211: 191-203. PubMed ID: 26459604 Summary: Fusion of individual myoblasts to form multinucleated myofibers constitutes a widely conserved program for growth of the somatic musculature. This study used electron microscopy methods to study this key form of cell-cell fusion during development of the indirect flight muscles (IFMs) of Drosophila melanogaster. It was found that IFM myoblast-myotube fusion proceeds in a stepwise fashion and is governed by apparent cross talk between transmembrane and cytoskeletal elements. Cell adhesion was found to be necessary for bringing myoblasts to within a minimal distance from the myotubes. The branched actin polymerization machinery acts subsequently to promote tight apposition between the surfaces of the two cell types and formation of multiple sites of cell-cell contact, giving rise to nascent fusion pores whose expansion establishes full cytoplasmic continuity. Given the conserved features of IFM myogenesis, this sequence of cell interactions and membrane events and the mechanistic significance of cell adhesion elements and the actin-based cytoskeleton are likely to represent general principles of the myoblast fusion process.

Loganathan, R., Lee, J. S., Wells, M. B., Grevengoed, E., Slattery, M. and Andrew, D. J. (2015). Ribbon regulates morphogenesis of the Drosophila embryonic salivary gland through transcriptional activation and repression. Dev Biol. PubMed ID: 26477561 Summary: Ribbon (Rib) controls cell shape/volume increases during elongation of the Drosophila salivary gland (SG), without effects on general SG cell attributes such as specification, proliferation and apoptosis and without compromising epithelial-specific morphological attributes. To identify the genes regulated by Rib, ChIP-seq analysis was performed in embryos driving expression of GFP-tagged Rib specifically in the SGs. Microarray analysis compared RNA samples from age-matched wild-type and rib null embryos. From the superposed ChIP-seq and microarray gene expression data, 60 genomic sites bound by Rib were identified that were likely to regulate SG-specific gene expression. Several of the identified Rib targets were identified by qRT-pCR and/or in situ hybridization. The results indicate that Rib regulates cell growth and tissue shape via a diverse array of targets through both transcriptional activation and repression. Furthermore, the results suggest that autoregulation of rib expression may be a key component of the SG morphogenetic gene network.

Seong, K.H., Tsuda, M., Tsuda-Sakurai, K. and Aigaki, T. (2015). The plant homeodomain finger protein MESR4 is essential for embryonic development in Drosophila. Genesis [Epub ahead of print]. PubMed ID: 26467775 Summary: Misexpression Suppressor of Ras 4 (MESR4), a PHD finger protein with nine zinc-finger motifs has been implicated in various biological processes including the regulation of fat storage and innate immunity in Drosophila. However, the role of MESR4 in the context of development remains unclear. This study shows that MESR4 is a nuclear protein essential for embryonic development. Immunostaining of polytene chromosomes using anti-MESR4 antibody revealed that MESR4 binds to numerous bands along the chromosome arms. The most intense signal was detected at the 39E-F region, which is known to contain the histone gene cluster. P-element insertions in the MESR4 locus are homozygous lethal during embryogenesis with defects in ventral ectoderm formation and head encapsulation. In the mutant embryos, expression of Fasciclin 3 (Fas3), an EGFR signal target gene is greatly reduced, and the level of EGFR signal-dependent double phosphorylated ERK (dp-ERK) remains low. However, in the context of wing vein formation, genetic interaction experiments suggest that MESR4 is involved in the EGFR signaling as a negative regulator. These results suggest that MESR4 is a novel chromatin-binding protein required for proper expression of genes including those regulated by the EGFR signaling pathway during development.

Zheng, C., Diaz-Cuadros, M. and Chalfie, M. (2015). Dishevelled attenuates the repelling activity of Wnt signaling during neurite outgrowth in Caenorhabditis elegans. Proc Natl Acad Sci U S A 112: 13243-13248. PubMed ID: 26460008 Summary: Wnt proteins regulate axonal outgrowth along the anterior-posterior axis, but the intracellular mechanisms that modulate the strength of Wnt signaling in axon guidance are largely unknown. Using the Caenorhabditis elegans mechanosensory PLM neurons, this study found that posteriorly enriched LIN-44/Wnt acts as a repellent to promote anteriorly directed neurite outgrowth through the LIN-17/Frizzled (see Drosophila Frizzled) receptor, instead of controlling neuronal polarity as previously thought. Dishevelled proteins (see Drosophila Dishevelled) DSH-1 and MIG-5 redundantly mediate the repulsive activity of the Wnt signals to induce anterior outgrowth, whereas DSH-1 also provides feedback inhibition to attenuate the signaling to allow posterior outgrowth against the Wnt gradient. This inhibitory function of DSH-1, which requires its dishevelled, Egl-10, and pleckstrin (DEP) domain, acts by promoting LIN-17 phosphorylation and is antagonized by planar cell polarity signaling components Van Gogh (VANG-1; see Drosophila Van Gogh) and Prickle (PRKL-1; see Drosophila Prickle). These results suggest that Dsh proteins both respond to Wnt signals to shape neuronal projections and moderate its activity to fine-tune neuronal morphology.

Wednesday, November 11th

Parker, J. and Struhl, G. (2015). Scaling the Drosophila wing: TOR-dependent target gene access by the Hippo pathway transducer Yorkie. Journal-PLoS Biol 13: e1002274. PubMed ID: 26474042 Summary: How cells integrate distinct inputs to generate organs of the appropriate size and shape is largely unknown. The transcriptional coactivator Yorkie (Yki, a YES-Associated Protein, or YAP) acts downstream of patterning morphogens and other tissue-intrinsic signals to promote organ growth. Yki activity is regulated primarily by the Warts/Hippo (Wts/Hpo) pathway, which impedes nuclear access of Yki by a cytoplasmic tethering mechanism. This study shows that the TOR pathway regulates Yki by a separate and novel mechanism in the Drosophila wing. Instead of controlling Yki nuclear access, TOR signaling governs Yki action after it reaches the nucleus by allowing it to gain access to its target genes. When TOR activity is inhibited, Yki accumulates in the nucleus but is sequestered from its normal growth-promoting target genes. TOR also promotes wing growth by liberating Yki from nuclear seclusion, a parallel pathway that is proposed to contribute to the scaling of wing size with nutrient availability.

Srivastava, A. (2015). A novel link between FMR gene and the JNK pathway provides clues to possible role in malignant pleural mesothelioma. FEBS Open Bio 5: 705-711. PubMed ID: 26425438 Summary: Malignant pleural mesothelioma (MPM) is an aggressive form of thoracic cancer with poor prognosis. While some studies have identified the molecular alterations associated with MPM, little is known about their role in MPM. For example, fragile X mental retardation (FMR) gene is up-regulated in MPM but its role in MPM is unknown. Utilizing Drosophila genetics, this study investigated the possible role FMR may be playing in MPM. Evidence is provided that suggests that FMR may contribute to tumorigenesis by up-regulating a matrix metalloprotease (MMP) and by degrading the basement membrane (BM), both important for tumor metastasis. A novel link between FMR and the JNK pathway was demonstrated and it was suggested that the effects of FMR in MPM could in part be mediated by up-regulation of the JNK pathway.

Ramirez, J., Martinez, A., Lectez, B., Lee, S. Y., Franco, M., Barrio, R., Dittmar, G. and Mayor, U. (2015). Proteomic analysis of the ubiquitin landscape in the Drosophila embryonic nervous system and the adult photoreceptor cells. PLoS One 10: e0139083. PubMed ID: 26460970 Summary: Ubiquitination is known to regulate physiological neuronal functions as well as to be involved in a number of neuronal diseases. Using an in vivo biotinylation strategy this study has isolated and identified the ubiquitinated proteome in neurons both for the developing embryonic brain and for the adult eye of Drosophila melanogaster. Bioinformatic comparison of both datasets indicates a significant difference on the ubiquitin substrates, which logically correlates with the processes that are most active at each of the developmental stages. Detection within the isolated material of two ubiquitin E3 ligases, Parkin and Ube3a, indicates their ubiquitinating activity on the studied tissues. Further identification of the proteins that do accumulate upon interference with the proteasomal degradative pathway provides an indication of the proteins that are targeted for clearance in neurons. Last, the proof-of-principle validation is reported of two lysine residues required for nSyb ubiquitination. These data cast light on the differential and common ubiquitination pathways between the embryonic and adult neurons, and hence will contribute to the understanding of the mechanisms by which neuronal function is regulated. The in vivo biotinylation methodology described in this study complements other approaches for ubiquitome study and offers unique advantages, and is poised to provide further insight into disease mechanisms related to the ubiquitin proteasome system.

Zhang, L., et al. (2015). Microenvironment-induced PTEN loss by exosomal microRNA primes brain metastasis outgrowth. Nature 527: 100-104. PubMed ID: 26479035 Summary: The development of life-threatening cancer metastases at distant organs requires disseminated tumour cells' adaptation to, and co-evolution with, the drastically different microenvironments of metastatic sites. Cancer cells of common origin manifest distinct gene expression patterns after metastasizing to different organs. It is unclear when and how disseminated tumour cells acquire the essential traits from the microenvironment of metastatic organs that prime their subsequent outgrowth. This study shows that both human and mouse tumour cells with normal expression of PTEN, an important tumour suppressor, lose PTEN expression after dissemination to the brain, but not to other organs. The PTEN level in PTEN-loss brain metastatic tumour cells is restored after leaving the brain microenvironment. This brain microenvironment-dependent, reversible PTEN messenger RNA and protein downregulation is epigenetically regulated by microRNAs from brain astrocytes. Mechanistically, astrocyte-derived exosomes mediate an intercellular transfer of PTEN-targeting microRNAs to metastatic tumour cells, while astrocyte-specific depletion of PTEN-targeting microRNAs or blockade of astrocyte exosome secretion rescues the PTEN loss and suppresses brain metastasis in vivo. These findings demonstrate a remarkable plasticity of PTEN expression in metastatic tumour cells in response to different organ microenvironments, underpinning an essential role of co-evolution between the metastatic cells and their microenvironment during the adaptive metastatic outgrowth.

Tuesday, November 10th

Pavot, P., Carbognin, E. and Martin, J. R. (2015). PKA and cAMP/CNG channels independently regulate the cholinergic Ca(2+)-response of Drosophila mushroom body neurons. eNeuro 2 [Epub ahead of print]. PubMed ID: 26464971 Summary: This work investigated the role of mushroom bodies (MBs) in olfactory learning and memory. Advantage was taken of in vivo bioluminescence imaging, which allowed real-time monitoring of the entire MBs (both the calyx/cell-bodies and the lobes) simultaneously. Neuronal Ca(2+)-activity was imaged continuously, over a long time period, and the nicotine-evoked Ca(2+)-response was caracterized. Using both genetics and pharmacological approaches to interfere with different components of the cAMP signaling pathway, it was first shown that the Ca(2+)-response is proportional to the levels of cAMP. Second, it was reveal that an acute change in cAMP levels is sufficient to trigger a Ca(2+)-response. Third, genetic manipulation of protein kinase A (PKA), a direct effector of cAMP, suggests that cAMP also has PKA-independent effects through the cyclic nucleotide-gated Ca(2+)-channel (CNG). Finally, the disruption of calmodulin, one of the main regulators of the rutabaga adenylate cyclase (AC), yields different effects in the calyx/cell-bodies and in the lobes, suggesting a differential and regionalized regulation of AC. These results provide insights into the complex Ca(2+)-response in the MBs, leading to the conclusion that cAMP modulates the Ca(2+)-responses through both PKA-dependent and -independent mechanisms, the latter through CNG-channels.

Roessingh, S., Wolfgang, W. and Stanewsky, R. (2015). Loss of Drosophila melanogaster TRPA1 function affects "siesta" behavior but not synchronization to temperature cycles. J Biol Rhythms [Epub ahead of print]. PubMed ID: 26459465 Summary: To maintain synchrony with the environment, circadian clocks use a wide range of cycling sensory cues that provide input to the clock (zeitgebers), including environmental temperature cycles (TCs). There is some knowledge about which clock neuronal groups are important for temperature synchronization, knowledge on the temperature receptors and their signaling pathways that feed temperature information to the (neuronal) clock is lacking. Since TRPA1 is a well-known thermosensor that functions in a range of temperature-related behaviors, and it is potentially expressed in clock neurons, this study set out to test the putative role of TRPA1 in temperature synchronization of the circadian clock. Flies lacking TRPA1 are still able to synchronize their behavioral activity to TCs comparable to wild-type flies, both in 16o C : 25o C and 20o C : 29o C TCs. In addition, it was found that flies lacking TRPA1 show higher activity levels during the middle of the warm phase of 20 o C : 29o C TCs, and it was show that this TRPA1-mediated repression of locomotor activity during the 'siesta' is caused by a lack of sleep. Based on these data, it is concluded that the TRPA1 channel is not required for temperature synchronization in this broad temperature range but instead is required to repress activity during the warm part of the day.

Kamiyama, D., McGorty, R., Kamiyama, R., Kim, M. D., Chiba, A. and Huang, B. (2015). Specification of dendritogenesis site in Drosophila aCC motoneuron by membrane enrichment of Pak1 through Dscam1. Dev Cell 35: 93-106. PubMed ID: 26460947 Summary: Precise positioning of dendritic branches is a critical step in the establishment of neuronal circuitry. However, there is limited knowledge on how environmental cues translate into dendrite initiation or branching at a specific position. Through a combination of mutation, RNAi, and imaging experiments, this study found that a Dscam-Dock-Pak1 hierarchical interaction defines the stereotypical dendrite growth site in the Drosophila aCC motoneuron. This interaction localizes the Cdc42 effector Pak1 to the plasma membrane at the dendrite initiation site before the activation of Cdc42. Ectopic expression of membrane-anchored Pak1 overrides this spatial specification of dendritogenesis, confirming its function in guiding Cdc42 signaling. It was further discovered that Dscam1 localization in aCC occurs through an inter-neuronal contact that involves Dscam1 in the partner MP1 neuron. These findings elucidate a mechanism by which Dscam1 controls neuronal morphogenesis through spatial regulation of Cdc42 signaling and, subsequently, cytoskeletal remodeling.

Fisher, Y. E., Silies, M. and Clandinin, T. R. (2015). Orientation selectivity sharpens motion detection in Drosophila.Neuron 88: 390-402. PubMed ID: 26456048 Summary: Detecting the orientation and movement of edges in a scene is critical to visually guided behaviors of many animals. What are the circuit algorithms that allow the brain to extract such behaviorally vital visual cues? Using in vivo two-photon calcium imaging in Drosophila, this study describes direction selective signals in the dendrites of T4 and T5 neurons, detectors of local motion. This circuit performs selective amplification of local light inputs, an observation that constrains motion detection models and confirms a core prediction of the Hassenstein-Reichardt correlator (HRC). These neurons are also orientation selective, responding strongly to static features that are orthogonal to their preferred axis of motion, a tuning property not predicted by the HRC. This coincident extraction of orientation and direction sharpens directional tuning through surround inhibition and reveals a striking parallel between visual processing in flies and vertebrate cortex, suggesting a universal strategy for motion processing.

Monday, November 9th

Eisman, R. C., Phelps, M. A. and Kaufman, T. (2015). An amino-terminal Polo kinase interaction motif acts in the regulation of centrosome formation and reveals a novel function for centrosomin (cnn) in Drosophila. Genetics 201: 685-706. PubMed ID: 26447129 Summary: The formation of the pericentriolar matrix (PCM) and a fully functional centrosome in syncytial Drosophila embryos requires the rapid transport of Cnn during initiation of the centrosome replication cycle. A Cnn and Polo kinase interaction is apparently required during embryogenesis and involves the exon 1A-initiating coding exon, suggesting a subset of Cnn splice variants is regulated by Polo kinase. During PCM formation exon 1A Cnn-Long Form proteins likely bind Polo kinase before phosphorylation by Polo for Cnn transport to the centrosome. Loss of either of these interactions in a portion of the total Cnn protein pool is sufficient to remove native Cnn from the pool, thereby altering the normal localization dynamics of Cnn to the PCM. Additionally, Cnn-Short Form proteins are required for polar body formation, a process known to require Polo kinase after the completion of meiosis. Exon 1A Cnn-LF and Cnn-SF proteins, in conjunction with Polo kinase, are required at the completion of meiosis and for the formation of functional centrosomes during early embryogenesis.

Christophorou, N., Rubin, T., Bonnet, I., Piolot, T., Arnaud, M. and Huynh, J. R. (2015). Microtubule-driven nuclear rotations promote meiotic chromosome dynamics. Nat Cell Biol 17: 1388-1400. PubMed ID: 26458247 Summary: At the onset of meiosis, each chromosome needs to find its homologue and pair to ensure proper segregation. In Drosophila, pairing occurs during the mitotic cycles preceding meiosis.This study shows that germ cell nuclei undergo marked movements during this developmental window. Microtubules and Dynein are driving nuclear rotations and are required for centromere pairing and clustering. It was further found that Klaroid (SUN) and Klarsicht (KASH) co-localize with centromeres at the nuclear envelope and are required for proper chromosome motions and pairing. Mud (NuMA in vertebrates) was identified as co-localizing with centromeres, Klarsicht and Klaroid. Mud is also required to maintain the integrity of the nuclear envelope and for the correct assembly of the synaptonemal complex. These findings reveal a mechanism for chromosome pairing in Drosophila, and indicate that microtubules, centrosomes and associated proteins play a crucial role in the dynamic organization of chromosomes inside the nucleus.

Drpic, D., Pereira, A. J., Barisic, M., Maresca, T. J. and Maiato, H. (2015). Polar ejection forces promote the conversion from lateral to end-on kinetochore-microtubule attachments on mono-oriented chromosomes. Cell Rep 13: 460-468. PubMed ID: 26456825 Summary: Chromosome bi-orientation occurs after conversion of initial lateral attachments between kinetochores and spindle microtubules into stable end-on attachments near the cell equator. After bi-orientation, chromosomes experience tension from spindle forces, which plays a key role in the stabilization of correct kinetochore-microtubule attachments. However, how end-on kinetochore-microtubule attachments are first stabilized in the absence of tension remains a key unanswered question. To address this, Drosophila S2 cells undergoing mitosis with unreplicated genomes (SMUGs) were generated. SMUGs retained single condensed chromatids that attached laterally to spindle microtubules. Over time, laterally attached kinetochores converted into end-on attachments and experienced intra-kinetochore stretch/structural deformation, and SMUGs eventually exited a delayed mitosis with mono-oriented chromosomes after satisfying the spindle-assembly checkpoint (SAC). Polar ejection forces (PEFs) generated by Chromokinesins promoted the conversion from lateral to end-on kinetochore-microtubule attachments that satisfied the SAC in SMUGs. Thus, PEFs convert lateral to stable end-on kinetochore-microtubule attachments, independently of chromosome bi-orientation.

Parker, D., Iyer, A., Shah, S., Moran, A., Hjelmeland, A., Basu, M. K., Liu, R. and Mitra, K. (2015). A novel mitochondrial pool of Cyclin E, regulated by Drp1, is linked to cell density dependent cell proliferation. J Cell Sci [Epub ahead of print]. PubMed ID: 26446260 Summary: The regulation and function of the crucial cell cycle regulator Cyclin E (CycE) remains elusive. Among other cyclins, CycE can be uniquely controlled by mitochondrial energetics, the exact mechanism being unclear. Using mammalian cells (in vitro) and Drosophila (in vivo) model systems in parallel this study shows that CycE can be directly regulated by mitochondria by its recruitment to the organelle. Active mitochondrial bioenergetics maintains a distinct mitochondrial pool of CycE (mtCycE) lacking a key phosphorylation required for its degradation. Loss of the mitochondrial fission protein Drp1 augments mitochondrial respiration and elevates the mtCycE-pool allowing CycE deregulation, cell cycle alterations and enrichment of stem cell markers. Such CycE deregulation after Drp1 loss attenuates cell proliferation in low cell density environments. However, in high cell density environments elevated MEK-ERK signaling in the absence of Drp1 releases mtCycE to support escape of contact inhibition and maintain aberrant cell proliferation. Such Drp1 driven regulation of CycE recruitment to mitochondria may be a mechanism to modulate CycE degradation during normal developmental processes as well as in tumorigenic events.

Sunday, November 8th

Yu, Y., Gu, J., Jin, Y., Luo, Y., Preall, J. B., Ma, J., Czech, B. and Hannon, G. J. (2015). Panoramix enforces piRNA-dependent cotranscriptional silencing. Science 350: 339-342. PubMed ID: 26472911 Summary: The Piwi-interacting RNA (piRNA) pathway is a small RNA-based innate immune system that defends germ cell genomes against transposons. In Drosophila ovaries, the nuclear Piwi protein is required for transcriptional silencing of transposons, though the precise mechanisms by which this occurs are unknown. This study show that the CG9754 protein is a component of Piwi complexes that functions downstream of Piwi and its binding partner, Asterix, in transcriptional silencing. Enforced tethering of CG9754 to nascent messenger RNA transcripts causes cotranscriptional silencing of the source locus and the deposition of repressive chromatin marks. CG9754 has been named "Panoramix," and it is proposed that this protein could act as an adaptor, scaffolding interactions between the piRNA pathway and the general silencing machinery that it recruits to enforce transcriptional repression.

Pek, J.W., Osman, I., Tay, M.L. and Zheng, R.T. (2015). Stable intronic sequence RNAs have possible regulatory roles in Drosophila melanogaster. J Cell Biol 211: 243-251. PubMed ID: 26504165 Summary: Stable intronic sequence RNAs (sisRNAs) have been found in Xenopus tropicalis, human cell lines, and Epstein-Barr virus; however, the biological significance of sisRNAs remains poorly understood. This study identified sisRNAs in Drosophila melanogaster by deep sequencing, reverse transcription polymerase chain reaction, and Northern blotting. A sisRNA (sisR-1) was characterized from the regena (rga) locus and was found to be processed from the precursor messenger RNA (pre-mRNA). A cis-natural antisense transcript (ASTR) from the rga locus was also documented that is highly expressed in early embryos. During embryogenesis, ASTR promotes robust rga pre-mRNA expression. Interestingly, sisR-1 represses ASTR, with consequential effects on rga pre-mRNA expression. These results suggest a model in which sisR-1 modulates its host gene expression by repressing ASTR during embryogenesis. The study proposes that sisR-1 belongs to a class of sisRNAs with probable regulatory activities in Drosophila.

Ryu, Y. H. and Macdonald, P. M. (2015). RNA sequences required for the noncoding function of oskar RNA also mediate regulation of Oskar protein expression by Bicoid Stability Factor. Dev Biol [Epub ahead of print]. PubMed ID: 26433064 Summary: The Drosophila oskar (osk) mRNA is unusual in having both coding and noncoding functions. As an mRNA, osk encodes a protein which is deployed specifically at the posterior of the oocyte. This spatially-restricted deployment relies on a program of mRNA localization and both repression and activation of translation, all dependent on regulatory elements located primarily in the 3' untranslated region (UTR) of the mRNA. The 3' UTR also mediates the noncoding function of osk, which is essential for progression through oogenesis. Mutations which most strongly disrupt the noncoding function are positioned in a short region (the C region) near the 3' end of the mRNA, in close proximity to elements required for activation of translation. This study show that Bicoid Stability Factor (BSF) binds specifically to the C region of the mRNA. Both knockdown of bsf and mutation of BSF binding sites in osk mRNA have the same consequences: Osk expression is largely eliminated late in oogenesis, with both mRNA localization and translation disrupted. Although the C region of the osk 3' UTR is required for the noncoding function, BSF binding does not appear to be essential for that function.

Germain, D. R., Li, L., Hildebrandt, M. R., Simmonds, A. J., Hughes, S. C. and Godbout, R. (2015). Loss of the Drosophila melanogaster DEAD box protein Ddx1 leads to reduced size and aberrant gametogenesis. Dev Biol [Epub ahead of print]. PubMed ID: 26433063 Summary: Mammalian DEAD box helicase DDX1 has been implicated in RNA trafficking, DNA double-strand break repair and RNA processing; however, little is known about its role during animal development. This study reports phenotypes associated with a null Ddx1 (Ddx1AX) mutation generated in Drosophila melanogaster. Ddx1 null flies are viable but significantly smaller than control and Ddx1 heterozygous flies. Female Ddx1 null flies have reduced fertility with egg chambers undergoing autophagy, whereas males are sterile due to disrupted spermatogenesis. Comparative RNA sequencing of control and Ddx1 null third instars identified several transcripts affected by Ddx1 inactivation. One of these, Sirup mRNA, was previously shown to be overexpressed under starvation conditions and implicated in mitochondrial function. This study demonstrates that Sirup is a direct binding target of Ddx1 and that Sirup mRNA is differentially spliced in the presence or absence of Ddx1. Combining Ddx1 null mutation with Sirup dsRNA-mediated knock-down causes epistatic lethality not observed in either single mutant. These data suggest a role for Drosophila Ddx1 in stress-induced regulation of splicing.

Saturday, November 7th

Rao, P.R., Lin, L., Huang, H., Guha, A., Roy, S. and Kornberg, T.B. (2015). Developmental compartments in the larval trachea of Drosophila. Elife [Epub ahead of print]. PubMed ID: 26491942 Summary: The Drosophila tracheal system is a branched tubular network that forms in the embryo by a post-mitotic program of morphogenesis. In third instar larvae (L3), cells constituting the second tracheal metamere (Tr2) reenter the cell cycle. Clonal analysis of L3 Tr2 reveals that dividing cells in the dorsal trunk, dorsal branch and transverse connective branches respect lineage restriction boundaries near branch junctions. These boundaries corresponded to domains of gene expression, for example where cells expressing Spalt, Delta and Serrate in the dorsal trunk meet vein-expressing cells in the dorsal branch or transverse connective. Notch signaling was activated to one side of these borders and was required for the identity, specializations and segregation of border cells. These findings suggest that Tr2 is comprised of developmental compartments and that developmental compartments are an organizational feature relevant to branched tubular networks.

Nikolova, L. S. and Metzstein, M. M. (2015). Intracellular lumen formation in Drosophila proceeds via a novel subcellular compartment. Development [Epub ahead of print]. PubMed ID: 26428009 Summary: To characterize the cellular mechanisms of subcellular tube formation, this study refined methods of high pressure freezing/freeze substitution to prepare Drosophila larvae for transmission electron microscopic (TEM) analysis. Using these methods, it was found that subcellular tracheal tube formation may proceed through a previously undescribed multimembrane intermediate composed of vesicles bound within a novel subcellular compartment. Correlative light/TEM procedures were developed to identify labeled cells in TEM-fixed larval samples. Using this technique, it was found that the vacuolar ATPase (V-ATPase) and the V-ATPase regulator Rabconnectin-3 are required for subcellular tube formation, probably in a step resolving the intermediate compartment into a mature lumen. In general, these methods should be applicable to analyzing the many cell biological problems which can be addressed using Drosophila larvae.

Diao, F., Mena, W., Shi, J., Park, D., Diao, F., Taghert, P., Ewer, J. and White, B. H. (2015). The Splice Isoforms of the Drosophila Ecdysis Triggering Hormone Receptor Have Developmentally Distinct Roles. Genetics [Epub ahead of print]. PubMed ID: 26534952 Summary: In order to grow, insects must periodically shed their exoskeletons. This process, called ecdysis, is initiated by the endocrine release of Ecdysis Triggering Hormone (ETH) and has been extensively studied as a model for understanding the hormonal control of behavior. Understanding how ETH regulates ecdysis behavior, however, has been impeded by limited knowledge of the hormone's neuronal targets. An alternatively spliced gene encoding a G-protein coupled receptor (ETHR) that is activated by ETH has been identified, and several lines of evidence support a role in ecdysis for its A-isoform. The function of a second ETHR isoform (ETHRB) remains unknown. This study used the recently introduced 'Trojan exon' technique to simultaneously mutate the ETHR gene and gain genetic access to the neurons that express its two isoforms. ETHRA and ETHRB were shown to be expressed in largely distinct subsets of neurons, and ETHRA- , but not ETHRB-expressing neurons are required for ecdysis at all developmental stages. However, both genetic and neuronal manipulations indicate an essential role for ETHRB at pupal and adult, but not larval, ecdysis. Several functionally important subsets of ETHR-expressing neurons were found including one that co-expresses the peptide Leucokinin and regulates fluid balance to facilitate ecdysis at the pupal stage. The general strategy of using a receptor gene as an entry point for genetic and neuronal manipulations should be useful in establishing patterns of functional connectivity in other hormonally regulated networks.

Llorens, J. V., Metzendorf, C., Missirlis, F. and Lind, M. I. (2015). Mitochondrial iron supply is required for the developmental pulse of ecdysone biosynthesis that initiates metamorphosis in Drosophila melanogaster. J Biol Inorg Chem [Epub ahead of print]. PubMed ID: 26468126 Summary: Synthesis of ecdysone, the key hormone that signals the termination of larval growth and the initiation of metamorphosis in insects, is carried out in the prothoracic gland by an array of iron-containing cytochrome P450s, encoded by the halloween genes. This study shows that mutants in Drosophila mitoferrin (dmfrn), the gene encoding a mitochondrial carrier protein implicated in mitochondrial iron import, fail to grow and initiate metamorphosis under dietary iron depletion or when ferritin function is partially compromised. In mutant dmfrn larvae reared under iron replete conditions, the expression of halloween genes is increased and 20-hydroxyecdysone (20E), the active form of ecdysone, is synthesized. In contrast, addition of an iron chelator to the diet of mutant dmfrn larvae disrupts 20E synthesis. Dietary addition of 20E has little effect on the growth defects, but enables approximately one-third of the iron-deprived dmfrn larvae to successfully turn into pupae and, in a smaller percentage, into adults. This partial rescue is not observed with dietary supply of ecdysone's precursor 7-dehydrocholesterol, a precursor in the ecdysone biosynthetic pathway. The findings reported in this study support the notion that a physiological supply of mitochondrial iron for the synthesis of iron-sulfur clusters and heme is required in the prothoracic glands of insect larvae for steroidogenesis. Furthermore, mitochondrial iron is also essential for normal larval growth.

Friday, November 6th

Bai, L. and Sehgal, A. (2015). Anaplastic lymphoma kinase acts in the Drosophila mushroom body to negatively regulate sleep. PLoS Genet 11: e1005611. PubMed ID: 26536237 Summary: Though evidence is mounting that a major function of sleep is to maintain brain plasticity and consolidate memory, little is known about the molecular pathways by which learning and sleep processes intercept. Anaplastic lymphoma kinase (Alk), the gene encoding a tyrosine receptor kinase whose inadvertent activation is the cause of many cancers, is implicated in synapse formation and cognitive functions. In particular, Alk genetically interacts with Neurofibromatosis 1 (Nf1) to regulate growth and associative learning in flies. This study shows that Alk mutants have increased sleep. Using a targeted RNAi screen the negative effects of Alk on sleep were located to the mushroom body, a structure important for both sleep and memory. Mutations in Nf1 were shown to produce a sexually dimorphic short sleep phenotype, and suppress the long sleep phenotype of Alk. Thus Alk and Nf1 interact in both learning and sleep regulation, highlighting a common pathway in these two processes.

Vogt, K., Yarali, A. and Tanimoto, H. (2015). Reversing stimulus timing in visual conditioning leads to memories with opposite valence in Drosophila. PLoS One 10: e0139797. PubMed ID: 26430885 Summary: Animals need to associate different environmental stimuli with each other regardless of whether they temporally overlap or not. Drosophila melanogaster displays olfactory trace conditioning, where an odor is followed by electric shock reinforcement after a temporal gap, leading to conditioned odor avoidance. Reversing the stimulus timing in olfactory conditioning results in the reversal of memory valence such that an odor that follows shock is later on approached (i.e. relief conditioning). This study explored the effects of stimulus timing on memory in another sensory modality, using a visual conditioning paradigm. Flies were found to form visual memories of opposite valence depending on stimulus timing and can associate a visual stimulus with reinforcement despite being presented with a temporal gap. These results suggest that associative memories with non-overlapping stimuli and the effect of stimulus timing on memory valence are shared across sensory modalities.

Pan, L., et al. (2015). Heterochromatin remodeling by CDK12 contributes to learning in Drosophila. Proc Natl Acad Sci U S A [Epub ahead of print]. PubMed ID: 26508632 Summary: Dynamic regulation of chromatin structure is required to modulate the transcription of genes in eukaryotes. However, the factors that contribute to the plasticity of heterochromatin structure are elusive. This study reports that cyclin-dependent kinase 12 (CDK12), a transcription elongation-associated RNA polymerase II (RNAPII) kinase, antagonizes heterochromatin enrichment in Drosophila chromosomes. Notably, loss of CDK12 induces the ectopic accumulation of heterochromatin protein 1 (HP1) on euchromatic arms, with a prominent enrichment on the X chromosome. Furthermore, ChIP and sequencing analysis reveals that the heterochromatin enrichment on the X chromosome mainly occurs within long genes involved in neuronal functions. Consequently, heterochromatin enrichment reduces the transcription of neuronal genes in the adult brain and results in a defect in Drosophila courtship learning. Taken together, these results define a previously unidentified role of CDK12 in controlling the epigenetic transition between euchromatin and heterochromatin and suggest a chromatin regulatory mechanism in neuronal behaviors.

Pathak, T., Agrawal, T., Richhariya, S., Sadaf, S. and Hasan, G. (2015). Store-operated calcium entry through Orai is required for transcriptional maturation of the flight circuit in Drosophila. J Neurosci 35: 13784-13799. PubMed ID: 26446229 Summary: Store operated calcium entry (SOCE) is thought to primarily regulate calcium homeostasis in neurons. Subsequent to identification of Orai as the SOCE channel in nonexcitable cells, investigation of Orai function in neurons demonstrated a requirement for SOCE in Drosophila flight. By analysis of an Orai mutant and by controlled expression of a dominant-negative Drosophila Orai transgene, this study shows that Orai-mediated SOCE is required in dopaminergic interneurons of the flight circuit during pupal development. Expression of dominant-negative Orai in dopaminergic neurons of pupae abolished flight. The loss of Orai-mediated SOCE alters transcriptional regulation of dopaminergic neurons, leading to downregulation of the enzyme tyrosine hydroxylase, which is essential for dopamine synthesis, and the dopamine transporter, which is required for dopamine uptake after synaptic release. These studies suggest that modulation of SOCE could serve as a novel mechanism for restoring dopamine levels in dopaminergic neurons.

Thursday, November 5th

Liu, Z., Yang, C. P., Sugino, K., Fu, C. C., Liu, L. Y., Yao, X., Lee, L. P. and Lee, T. (2015). . Opposing intrinsic temporal gradients guide neural stem cell production of varied neuronal fates. Science 350: 317-320. PubMed ID: 26472907 Summary: Neural stem cells show age-dependent developmental potentials, as evidenced by their production of distinct neuron types at different developmental times. Drosophila neuroblasts produce long, stereotyped lineages of neurons. This study sought factors that could regulate neural temporal fate by RNA-sequencing lineage-specific neuroblasts at various developmental times. Two RNA-binding proteins, IGF-II mRNA-binding protein (Imp) and Syncrip (Syp), display opposing high-to-low and low-to-high temporal gradients with lineage-specific temporal dynamics. Imp and Syp promote early and late fates, respectively, in both a slowly progressing and a rapidly changing lineage. Imp and Syp control neuronal fates in the mushroom body lineages by regulating the temporal transcription factor Chinmo translation. Together, the opposing Imp/Syp gradients encode stem cell age, specifying multiple cell fates within a lineage.

Özel, M.N., Langen, M., Hassan, B.A. and Hiesinger, P.R. (2015). Filopodial dynamics and growth cone stabilization in Drosophila visual circuit development. Elife [Epub ahead of print]. PubMed ID: 26512889 Summary: Filopodial dynamics are thought to control growth cone guidance, but the types and roles of growth cone dynamics underlying neural circuit assembly in a living brain are largely unknown. To address this issue, this study developed long-term, continuous, fast and high-resolution imaging of growth cone dynamics from axon growth to synapse formation in cultured Drosophila brains. Using R7 photoreceptor neurons as a model it was shown that >90% of the growth cone filopodia exhibit fast, stochastic dynamics that persist despite ongoing stepwise layer formation. Correspondingly, R7 growth cones stabilize early and change their final position by passive dislocation. N-Cadherin controls both fast filopodial dynamics and growth cone stabilization. Surprisingly, loss of N-Cadherin causes no primary targeting defects, but destabilizes R7 growth cones to jump between correct and incorrect layers. Hence, growth cone dynamics can influence wiring specificity without a direct role in target recognition and implement simple rules during circuit assembly.

Lincoln, B.L., Alabsi, S.H., Frendo, N., Freund, R. and Keller, L.C. (2015). Drosophila neuronal injury follows a temporal sequence of cellular events leading to degeneration at the neuromuscular junction. J Exp Neurosci 9(Suppl 2): 1-9. PubMed ID: 26512206 Summary: Neurodegenerative diseases affect millions of people worldwide, and as the global population ages, there is a critical need to improve understanding of the molecular and cellular mechanisms that drive neurodegeneration. At the molecular level, neurodegeneration involves the activation of complex signaling pathways that drive the active destruction of neurons and their intracellular components. This study uses an in vivo motor neuron injury assay to acutely induce neurodegeneration in order to follow the temporal order of events that occur following injury in Drosophila melanogaster. It was found that sites of injury can be rapidly identified based on structural defects to the neuronal cytoskeleton that result in disrupted axonal transport. Additionally, the neuromuscular junction accumulates ubiquitinated proteins prior to the neurodegenerative events, occurring at 24 hours post injury. These data provide insights into the early molecular events that occur during axonal and neuromuscular degeneration in a genetically tractable model organism. Importantly, the mechanisms that mediate neurodegeneration in flies are conserved in humans. Thus, these studies have implications for the understanding of the cellular and molecular events that occur in humans and will facilitate the identification of biomedically relevant targets for future treatments.

Giles, A. C., Opperman, K. J., Rankin, C. H. and Grill, B. (2015). Developmental function of the PHR protein RPM-1 is required for learning in Caenorhabditis elegans. G3 (Bethesda) [Epub ahead of print]. PubMed ID: 26464359 Summary: The PAM/Highwire/RPM-1 (PHR) proteins are signaling hubs that function as important regulators of neural development. Loss of function in C. elegans E3 ubiquitin-protein ligase rpm-1 and Drosophila Highwire results in failed axon termination, inappropriate axon targeting, and abnormal synapse formation. Very mild abnormalities in behavior have been found in animals lacking PHR protein function. Therefore, it was hypothesized that large defects in behavior might only be detected in scenarios in which evoked, prolonged circuit function is required, or in which behavioral plasticity occurs. rpm-1 loss-of-function mutants had relatively mild abnormalities in exploratory locomotion, but exhibited large defects in evoked responses to harsh touch and learning associated with tap habituation. Rescue analysis indicated that RPM-1 function in the mechanosensory neurons affects habituation. Transgenic expression of RPM-1 in adult animals failed to rescue habituation defects, consistent with developmental defects in rpm-1 mutants resulting in impaired habituation. Genetic analysis showed that other regulators of neuronal development that function in the rpm-1 pathway (including glo-4, fsn-1, and dlk-1) also affected habituation. Overall, these findings suggest that developmental defects in rpm-1 mutants manifest most prominently in behaviors that require protracted or plastic circuit function, such as learning.

Wednesday, November 4th

Lim, Y.M., Yagi, Y. and Tsuda, L. (2015). Cellular defense and sensory cell survival require distinct functions of ebi in Drosophila. PLoS One 10: e0141457. PubMed: 26524764 Summary: The innate immune response and stress-induced apoptosis are well-established signaling pathways related to cellular defense. NF-κB and AP-1 are redox-sensitive transcription factors that play important roles in those pathways. This study shows that Ebi, a Drosophila homolog of the mammalian co-repressor molecule transducin β-like 1 (TBL1), variously regulates the expression of specific genes that are targets of redox-sensitive transcription factors. In response to different stimuli, Ebi activates gene expression to support the acute immune response in fat bodies, whereas Ebi represses genes that are involved in apoptosis in photoreceptor cells. Thus, Ebi seems to act as a regulatory switch for genes that are activated or repressed in response to different external stimuli. These results offer clear in vivo evidence that the Ebi-containing co-repressor complex acts in a distinct manner to regulate transcription that is required for modulating the output of various processes during Drosophila development.

Momiuchi, Y., Kumada, K., Kuraishi, T., Takagaki, T., Aigaki, T., Oshima, Y. and Kurata, S. (2015). Role of phylogenetically conserved co-chaperone protein Droj2/DNAJA3 in NF-kappaB signaling. J Biol Chem [Epub ahead of print]. PubMed ID: 26245905 Summary: The nuclear factor κ B (NF-κB) pathway is a phylogenetically conserved signaling pathway with a central role in inflammatory and immune responses. This study demonstrates that a co-chaperone protein, Droj2/DNAJA3, is involved in the activation of canonical NF-κB signaling in flies and in human cultured cells. Overexpression of Droj2 induced the expression of an antimicrobial peptide in Drosophila. Conversely, Droj2 knockdown resulted in reduced expression of antimicrobial peptides and higher susceptibility to Gram-negative bacterial infection in flies. Similarly, Toll-like receptor-stimulated inhibitor of κB (IκB) phosphorylation and NF-κB activation was suppressed by DNAJA3 knockdown in human embryonic kidney 293 cells. IκB kinase overexpression-induced NF-κB phosphorylation was also compromised in the DNAJA3-knockdown cells. This study reveals a novel conserved regulator of the NF-κB pathway acting at the level of IκB phosphorylation.

Kanoh, H., Tong, L.L., Kuraishi, T., Suda, Y., Momiuchi, Y., Shishido, F. and Kurata, S. (2015). Genome-wide RNAi screening implicates the E3 ubiquitin ligase Sherpa in mediating innate immune signaling by Toll in Drosophila adults. Sci Signal 8: ra107. PubMed ID: 26508789 Summary: The Drosophila Toll pathway plays important roles in innate immune responses against Gram-positive bacteria and fungi. To identify previously uncharacterized components of this pathway, this study performed comparative, ex vivo, genome-wide RNA interference screening. In four screens, the Toll adaptor protein dMyd88, the downstream kinase Pelle, or the nuclear factor κB (NF-κB) homolog Dif were overexpressed, or Cactus, the Drosophila homolog of mammalian inhibitor of NF-κB was knocked down. On the basis of these screens, the E3 ubiquitin ligase Sherpa was identified as being necessary for the activation of Toll signaling. A loss-of-function sherpa mutant fly exhibits compromised production of antimicrobial peptides and enhances susceptibility to infection by Gram-positive bacteria. In cultured cells, Sherpa mediated ubiquitylation of dMyd88 and Sherpa itself, and Sherpa and Drosophila SUMO (small ubiquitin-like modifier) are required for the proper membrane localization of an adaptor complex containing dMyd88. These findings highlight a role for Sherpa in Drosophila host defense and suggest the SUMOylation-mediated regulation of dMyd88 functions in Toll innate immune signaling.

Kanoh, H., Kuraishi, T., Tong, L. L., Watanabe, R., Nagata, S. and Kurata, S. (2015). Ex vivo genome-wide RNAi screening of the Drosophila Toll signaling pathway elicited by a larva-derived tissue extract. Biochem Biophys Res Commun 467: 400-406. PubMed ID: 26427875 Summary: Damage-associated molecular patterns (DAMPs), so-called "danger signals," play important roles in host defense and pathophysiology in mammals and insects. In Drosophila, the Toll pathway confers damage responses during bacterial infection and improper cell-fate control. However, the intrinsic ligands and signaling mechanisms that potentiate innate immune responses remain unknown. This study demonstrate that a Drosophila larva-derived tissue extract strongly elicits Toll pathway activation via the Toll receptor. Using this extract, an ex vivo genome-wide RNAi screening was performed in Drosophila cultured cells, and several signaling factors were identified that are required for host defense and antimicrobial-peptide expression in Drosophila adults. These results suggest that the larva-derived tissue extract contains active ingredients that mediate Toll pathway activation, and the screening data will shed light on the mechanisms of damage-related Toll pathway signaling in Drosophila.

Takahashi, D., Garcia, B. L. and Kanost, M. R. (2015). Initiating protease with modular domains interacts with beta-glucan recognition protein to trigger innate immune response in insects. Proc Natl Acad Sci U S A. PubMed ID: 26504233 Summary: The autoactivation of an initiating serine protease upon binding of pattern recognition proteins to pathogen surfaces is a crucial step in eliciting insect immune responses such as the activation of Toll and prophenoloxidase pathways. However, the molecular mechanisms responsible for autoactivation of the initiating protease remains poorly understood. This study investigated the molecular basis for the autoactivation of hemolymph protease 14 (HP14), an initiating protease in hemolymph of Manduca sexta, upon the binding of beta-1,3-glucan by its recognition protein, βGRP2. Biochemical analysis using HP14 zymogen (proHP14), βGRP2, and the recombinant proteins as truncated forms showed that the amino-terminal modular low-density lipoprotein receptor class A (LA) domains within HP14 are required for proHP14 autoactivation that is stimulated by its interaction with βGRP2. Consistent with this result, recombinant LA domains inhibit the activation of proHP14 and prophenoloxidase, likely by competing with the interaction between βGRP2 and LA domains within proHP14. LA domains directly interact with βGRP2 in a calcium-dependent manner, and high-affinity interaction requires the C-terminal glucanase-like domain of βGRP2. Importantly, the affinity of LA domains for βGRP2 increases nearly 100-fold in the presence of beta-1,3-glucan. Taken together, these results present the first experimental evidence LA domains of an insect modular protease and glucanase-like domains of a βGRP mediate their interaction, and that this binding is essential for the protease autoactivation. Thus, this study provides important insight into the molecular basis underlying the initiation of protease cascade in insect immune responses.

Wang, Y. H., Hu, Y., Xing, L. S., Jiang, H., Hu, S. N., Raikhel, A. S. and Zou, Z. (2015). A critical role for CLSP2 in the modulation of antifungal immune response in mosquitoes. PLoS Pathog 11: e1004931. PubMed ID: 26057557 Summary: Entomopathogenic fungi represent a promising class of bio-insecticides for mosquito control. Thus, detailed knowledge of the molecular mechanisms governing anti-fungal immune response in mosquitoes is essential. This study shows that CLSP2, a serine protease with lectin domains, is a modulator of immune responses during anti-fungal infection in the mosquito Aedes aegypti. With a fungal infection, the expression of the CLSP2 gene is elevated. CLSP2 is cleaved upon challenge with Beauveria bassiana conidia, and the liberated CLSP2 C-terminal galactose-type C-type lectin (CTL)-type domain binds to fungal cell components and B. bassiana conidia. Furthermore, CLPS2 RNA interference silencing significantly increases the resistance to the fungal challenge. RNA-sequencing transcriptome analysis showed that the majority of immune genes were highly upregulated in the CLSP2-depleted mosquitoes infected with the fungus. The up-regulated immune gene cohorts belong to melanization and Toll pathways, but not to the IMD or JAK-STAT. The unique interaction of CLSP2 with Cactus suggests that it contributes in the control of AMP gene activation. Moreover, the abolishment of activation of AMPs, brought by iCLSP2 by the double knockdown of CLSP2 and Rel1, indicates that Rel1 mediates the action of CLSP2 on these immune genes. A thioester-containing protein (TEP22), a member of alpha2-macroglobulin family, has been implicated in the CLSP2-modulated mosquito antifungal defense. This study has contributed to a greater understanding of immune-modulating mechanisms in mosquitoes.

Tuesday, November 3rd

Garbe, D.S., Bollinger, W.L., Vigderman, A., Masek, P., Gertowski, J., Sehgal, A. and Keene, A.C. (2015). Context-specific comparison of sleep acquisition systems in Drosophila. Biol Open [Epub ahead of print]. PubMed ID: 26519516 Summary: Sleep is conserved across phyla and can be measured through electrophysiological or behavioral characteristics. The fruit fly, Drosophila melanogaster, provides an excellent model for investigating the genetic and neural mechanisms that regulate sleep. Multiple systems exist for measuring fly activity, including video analysis and single-beam (SB) or multi-beam (MB) infrared (IR)-based monitoring. This study compared multiple sleep parameters of individual flies using a custom-built video-based acquisition system, and commercially available SB- or MB-IR acquisition systems. It was found that all three monitoring systems appear sufficiently sensitive to detect changes in sleep duration associated with diet, age, and mating status. It was also demonstrated that MB-IR detection appears more sensitive than the SB-IR for detecting baseline nuances in sleep architecture, while architectural changes associated with varying life-history and environment are generally detected across all acquisition types. Finally, video recording of flies in an arena allows measurement of the effect of ambient environment on sleep. These experiments demonstrate a robust effect of arena shape and size as well as light levels on sleep duration and architecture, and highlighting the versatility of tracking-based sleep acquisition. These findings provide insight into the context-specific basis for choosing between Drosophila sleep acquisition systems, describe a novel cost-effective system for video tracking, and characterize sleep analysis using the MB-IR sleep analysis. Further, the study also describes a modified dark-place preference sleep assay using video tracking, confirming that flies prefer to sleep in dark locations.

Medina, I., Casal, J. and Fabre, C.C. (2015). Do circadian genes and ambient temperature affect substrate-borne signalling during Drosophila courtship? Biol Open [Epub ahead of print]. PubMed ID: 26519517 Summary: Courtship vibratory signals can be air-borne or substrate-borne. They convey distinct and species-specific information from one individual to its prospective partner. This study focuses on the substrate-borne vibratory signals generated by the abdominal quivers of the Drosophila male during courtship; these vibrations travel through the ground towards courted females and coincide with female immobility. It is not known which physical parameters of the vibrations encode the information that is received by the females and induces them to pause. The intervals between each vibratory pulse were examined, a feature that was reported to carry information for animal communication. However, evidence of periodic variations in the lengths of these intervals could not be found, as has been reported for fly acoustical signals. Because it has been suggested that the genes involved in the circadian clock may also regulate shorter rhythms, effects of period on the interval lengths were determined. Males that were mutant for the period gene produce vibrations with significantly altered interpulse intervals; also, treating wild type males with constant light results in similar alterations to the interpulse intervals. These results suggest that both the clock and light/dark cycles have input into the interpulse intervals of these vibrations. By altering the interpulse intervals by other means, it was found that ambient temperature also has a strong effect. However, behavioural analysis suggests that only extreme ambient temperatures can affect the strong correlation between female immobility and substrate-borne vibrations.

Lin, C. C., Prokop-Prigge, K. A., Preti, G. and Potter, C. J. (2015). Food odors trigger males to deposit a pheromone that guides aggregation and female oviposition decisions. Elife 4. PubMed ID: 26422512 Summary: Animals use olfactory cues for navigating complex environments. Food odors in particular provide crucial information regarding potential foraging sites. Many behaviors occur at food sites, yet how food odors regulate such behaviors at these sites is unclear. Using Drosophila melanogaster as an animal model, this study found that males deposit the pheromone 9-tricosene upon stimulation with the food-odor apple cider vinegar. This pheromone acts as a potent aggregation pheromone and as an oviposition guidance cue for females. Genetic, molecular, electrophysiological, and behavioral approaches were used to show that 9-tricosene activates antennal basiconic Or7a receptors, a receptor activated by many alcohols and aldehydes such as the green leaf volatile E2-hexenal. Loss of Or7a+ neurons or the Or7a receptor abolishes aggregation behavior and oviposition site-selection towards 9-tricosene and E2-hexenal. 9-Tricosene thus functions via Or7a to link food-odor perception with aggregation and egg-laying decisions.

Sellami, A. and Veenstra, J. A. (2015). SIFamide acts on fruitless neurons to modulate sexual behavior in Drosophila melanogaster. Peptides [Epub ahead of print]. PubMed ID: 26469541 Summary: The Drosophila gene fruitless expresses male and female specific transcription factors which are responsible for the generation of male specific neuronal circuitry for courtship behavior. Mutations in this gene may lead to bisexual behavior in males. Bisexual behavior in males also occurs in the absence of the neuropeptide SIFamide. SIFamide neurons do not express fruitless. However, when fruitless neurons are made to express RNAi specific for the SIFamide receptor, male flies engage in bisexual behavior, showing that SIFamide acts on fruitless neurons. If neurons expressing a SIFaR-gal4 transgene are killed by the apoptotic protein Reaper or when these neurons express SIFamide receptor RNAi, males also show male-male courtship behavior. This transgene was used to localize neurons that express the SIFamide receptor. Such neurons are ubiquitously present in the central nervous, and two neurons were also found in the uterus that project into the central nervous system.

Monday, November 2nd

Jia, M., Shan, Z., Yang, Y., Liu, C., Li, J, Luo, Z.G., Zhang, M., Cai, Y., Wen, W. and Wang, W. (2015). The structural basis of Miranda-mediated Staufen localization during Drosophila neuroblast asymmetric division. Nat Commun 6: 8381. PubMed ID: 26423004 Summary: During the asymmetric division of Drosophila neuroblasts (NBs), the scaffold Miranda (Mira) coordinates the subcellular distribution of cell-fate determinants including Staufen (Stau) and segregates them into the ganglion mother cells (GMCs). This study shows that the fifth double-stranded RNA (dsRNA)-binding domain (dsRBD5) of Stau is necessary and sufficient for binding to a coiled-coil region of Mira cargo-binding domain (CBD). The crystal structure of Mira514-595/Stau dsRBD5 complex illustrates that Mira forms an elongated parallel coiled-coil dimer, and two dsRBD5 symmetrically bind to the Mira dimer through their exposed β-sheet faces, revealing a previously unrecognized protein interaction mode for dsRBDs. It was further demonstrated that the Mira-Stau dsRBD5 interaction is responsible for the asymmetric localization of Stau during Drosophila NB asymmetric divisions. Finally, it was found that the CBD-mediated dimer assembly is likely a common requirement for Mira to recognize and translocate other cargos including brain tumour (Brat).

Geyer, A., Koltsaki, I., Hessinger, C., Renner, S. and Rogulja-Ortmann, A. (2015). Impact of Ultrabithorax alternative splicing on Drosophila embryonic nervous system development. Mech Dev [Epub ahead of print]. PubMed ID: 26299253 Summary: Hox genes control divergent segment identities along the anteroposterior body axis of bilateral animals by regulating a large number of processes in a cell context-specific manner. How Hox proteins achieve this functional diversity is a long-standing question in developmental biology. This study investigated the role of alternative splicing in functional specificity of the Drosophila Hox gene Ultrabithorax (Ubx). Focus was placed specifically on the embryonic central nervous system (CNS), and a description is provided of temporal expression patterns of three major Ubx isoforms during development of this tissue. These analyses imply distinct functions for individual isoforms in different stages of neural development. The set of Ubx isoforms expressed in two isoform-specific Ubx mutant strains was analyzed along with an analysis of the effects of splicing defects on regional neural stem cell (neuroblast) identity. These findings support the notion of specific isoforms having different effects in providing individual neuroblasts with positional identity along the anteroposterior body axis, as well as being involved in regulation of progeny cell fate.

Brown, H. E., Reichert, M. C. and Evans, T. A. (2015). Slit binding via the Ig1 domain is essential for midline repulsion by Drosophila Robo1 but dispensable for receptor expression, localization, and regulation in vivo. G3 (Bethesda) [Epub ahead of print]. PubMed ID: 26362767 Summary: This study examined the in vivo functional importance of the Ig1 domain of the Drosophila Roundabout1 receptor, which controls midline crossing of axons in response to Slit produced by the embryonic midline. Deleting Ig1 from Robo1 disrupts Slit binding in cultured Drosophila cells, and that a Robo1 variant lacking Ig1 (Robo1Ig1) is unable to promote ectopic midline repulsion in gain of function studies in the Drosophila embryonic CNS. The Ig1 domain is not required for proper expression, axonal localization, or Commissureless (Comm)-dependent regulation of Robo1 in vivo, and a genetic rescue assay was used to show that Robo1Ig1 is unable to substitute for full-length Robo1 to properly regulate midline crossing of axons. These results establish a direct link between in vitro biochemical studies of Slit-Robo interactions and in vivo genetic studies of Slit-Robo signaling during midline axon guidance, and distinguish Slit-dependent from Slit-independent aspects of Robo1 expression, regulation, and activity during embryonic development.

Kumar, R., Chotaliya, M., Vuppala, S., Auradkar, A., Palasamudrum, K. and Joshi, R. (2015). Role of Homothorax in region specific regulation of Deformed in embryonic neuroblasts. Mech Dev [Epub ahead of print]. PubMed ID: 26409112 Summary: The expression and regulation of Hox genes in developing central nervous system (CNS) lack important details like specific cell types where Hox genes are expressed and the transcriptional regulatory players involved in these cells. This study has investigated the expression and regulation of Drosophila Hox gene Deformed (Dfd) in specific cell types of embryonic CNS. Using Dfd neural autoregulatory enhancer, it was found that Dfd autoregulates itself in cells of mandibular neuromere. The role was investigated of a Hox cofactor Homothorax (Hth) for its role in regulating Dfd expression in CNS. Hth was found to exhibit a region specific role in controlling the expression of Dfd, but has no direct role in mandibular Dfd neural autoregulatory circuit. These results also suggest that homeodomain of Hth is not required for regulating Dfd expression in embryonic CNS.

Sunday, November 1st

Zhang, Z. and Presgraves, D.C. (2015). Drosophila X-linked genes have lower translation rates than autosomal genes. Mol Biol Evol [Epub ahead of print]. PubMed ID: 26486873 Summary: In Drosophila, X-linked and autosomal genes achieve comparable expression at the mRNA level. Whether comparable X-autosome gene expression is realized at the translational and, ultimately, the protein levels is however unknown. Previous studies suggest the possibility of higher translation rates for X-linked genes owing to stronger usage of preferred codons. This study uses public ribosome profiling data from Drosophila melanogaster to infer translation rates on the X chromosome versus the autosomes. It was found that X-linked genes have consistently lower ribosome densities than autosomal genes in S2 cells, early embryos, eggs, and mature oocytes. Surprisingly, the lower ribosome densities of X-linked genes are not consistent with faster translation elongation but instead imply slower translation initiation. In particular, X-linked genes have sequence features known to slow translation initiation such as stronger mRNA structure near start codons and longer 5' UTRs. Comparison to outgroup species suggests that stronger mRNA structure is an evolved feature of Drosophila X chromosomes. Finally, it was found that the magnitude of the X-autosome difference in ribosome densities is smaller for genes encoding members of protein complexes, suggesting that stoichiometry constrains the evolution of translation rates. In sum, these analyses suggest that Drosophila X-linked genes have evolved lower translation rates than autosomal genes despite stronger usage of preferred codons.

Calvo-Martín, J.M., Librado, P., Aguadé, M., Papaceit, M. and Segarra, C. (2015). Adaptive selection and coevolution at the proteins of the Polycomb repressive complexes in Drosophila. Heredity (Edinb) [Epub ahead of print]. PubMed ID: 26486609 Summary: Polycomb group (PcG) proteins are important epigenetic regulatory proteins that modulate the chromatin state through posttranslational histone modifications. These interacting proteins form multimeric complexes that repress gene expression. Thus, PcG proteins are expected to evolve coordinately, which might be reflected in their phylogenetic trees by concordant episodes of positive selection and by a correlation in evolutionary rates. In order to detect these signals of coevolution, this study analyzed the molecular evolution of 17 genes encoding the subunits of five Polycomb repressive complexes in the Drosophila genus. The observed distribution of divergence differs substantially among and along proteins. Indeed, CAF1 is uniformly conserved, whereas only the established protein domains are conserved in other proteins, such as PHO, PHOL, PSC, PH-P and ASX. Moreover, regions with a low divergence not yet described as protein domains are present, for instance, in SFMBT and SU(Z)12. Maximum likelihood methods indicate an acceleration in the nonsynonymous substitution rate at the lineage ancestral to the obscura group species in most genes encoding subunits of the Pcl-PRC2 complex and in genes Sfmbt, Psc and Kdm2. These methods also allow inferring the action of positive selection in this lineage at genes E(z) and Sfmbt. Finally, the protein interaction network predicted from the complete proteomes of 12 Drosophila species using a coevolutionary approach shows two tight PcG clusters. These clusters include well-established binary interactions among PcG proteins as well as new putative interactions.

Vedanayagam, J. P. and Garrigan, D. (2015). The effects of natural selection across molecular pathways in Drosophila melanogaster. BMC Evol Biol 15: 203. PubMed ID: 26391223 Summary: Whole-genome RNA interference post-transcriptional silencing (RNAi) is a widely used method for studying the phenotypic effects of knocking down individual genes. This study used a population genomic approach to characterize the rate of evolution for proteins affecting 26 RNAi knockdown phenotypes in Drosophila melanogaster. Only two of the 26 RNAi knockdown phenotypes are enriched for rapidly evolving proteins: innate immunity and regulation of Hedgehog signaling. Among all genes associated with an RNAi knockdown phenotype, examples were noted in which the adaptively evolving proteins play a well-defined role in a given molecular pathway. However, most adaptively evolving proteins are found to perform more general cellular functions. When RNAi phenotypes are grouped into categories according to cellular function, it was found that genes involved in the greatest number of phenotypic categories are also significantly more likely to have a history of rapid protein evolution. Genes that have been demonstrated to have a measurable effect on multiple molecular phenotypes show higher rates of protein evolution than genes having an effect on a single category of phenotype. Defining pleiotropy in this way yields very different results than previous studies that define pleiotropy by the number of physical interactions, which show highly connected proteins tend to evolve more slowly than lowly connected proteins. It is suggested that a high degree of pleiotropy may increase the likelihood of compensatory substitution, consistent with modern theoretical work on adaptation.

Yee, W. K., Rogell, B., Lemos, B. and Dowling, D. K. (2015). Intergenomic interactions between mitochondrial and Y-linked genes shape male mating patterns and fertility in Drosophila melanogaster. Evolution [Epub ahead of print]. PubMed ID: 26419212 Summary: Under maternal inheritance, mitochondrial genomes are prone to accumulate mutations that exhibit male-biased effects. Such mutations should, however, place selection on the nuclear genome for modifier adaptations that mitigate mitochondrial-incurred male harm. One gene region that might harbor such modifiers is the Y-chromosome, given the abundance of Y-linked variation for male fertility, and because Y-linked modifiers would not exert antagonistic effects in females because they would be found only in males. Recent studies in Drosophila revealed a set of nuclear genes whose expression is sensitive to allelic variation among mtDNA- and Y-haplotypes, suggesting these genes might be entwined in evolutionary conflict between mtDNA and Y. This study tested whether genetic variation across mtDNA and Y haplotypes, sourced from three disjunct populations, interacts to affect male mating patterns and fertility across 10 days of early life in D. melanogaster. Whether coevolved mito-Y combinations outperform their evolutionarily novel counterparts, as predicted if the interacting Y-linked variance is comprised of modifier adaptations, was also tested. Although no evidence was found that coevolved mito-Y combinations outperformed their novel counterparts, interactions between mtDNA and Y-chromosomes affected male mating patterns. These interactions were dependent on male age; thus male reproductive success was shaped by G x G x E interactions.

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