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https://www.readbyqxmd.com/read/27932387/the-long-non-coding-rna-transcriptome-of-dictyostelium-discoideum-development
#1
Rafael D Rosengarten, Balaji Santhanam, Janez Kokosar, Gad Shaulsky
Dictyostelium discoideum live in the soil as single cells, engulfing bacteria and growing vegetatively. Upon starvation, tens of thousands of amoebae enter a developmental program that includes aggregation, multicellular differentiation, and sporulation. Major shifts across the protein-coding transcriptome accompany these developmental changes. However, no study has presented a global survey of long non-coding RNAs in D. discoideum To characterize the antisense and long intergenic non-coding RNA transcriptome, we analyzed previously published developmental time course samples using an RNA-sequencing library preparation method that selectively depletes ribosomal RNAs...
December 7, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27923724/strain-specific-impact-of-the-high-pathogenicity-island-on-virulence-in-extra-intestinal-pathogenic-escherichia-coli
#2
Mounira Smati, Giuseppe Magistro, Sandrine Adiba, Andreas Wieser, Bertrand Picard, Sören Schubert, Erick Denamur
In order to clarify the role of the high-pathogenicity island (HPI) in the experimental virulence of Escherichia coli, we constructed different deletion mutants of the entire HPI and of three individual genes (irp2, fyuA and ybtA), encoding for three main functions within the HPI. Those mutants were constructed for three phylogroup B2 strains (536-STc127, CFT073-STc73, and NU14-STc95), representative of the main B2 subgroups causing extra-intestinal infections. Transcriptional profiles obtained for the selected HPI genes irp2, fyuA and ybtA revealed similar patterns for all strains, both under selective iron-deplete conditions and in intracellular bacterial communities in vitro, with a high expression of irp2...
November 22, 2016: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/27919433/sodc-modulates-ras-and-pkb-signaling-in-dictyostelium
#3
Boris Castillo, Seon-Hee Kim, Mujataba Sharief, Tong Sun, Lou W Kim
We have previously reported that the basal RasG activity is aberrantly high in cells lacking Superoxide dismutase C (SodC). Here we report that other Ras proteins such as RasC and RasD activities are not affected in sodC(-) cells and mutagenesis studies showed that the presence of the Cys(118) in the Ras proteins is essential for the superoxide-mediated activation of Ras proteins in Dictyostelium. In addition to the loss of SodC, lack of extracellular magnesium ions increased the level of intracellular superoxide and active RasG proteins...
November 30, 2016: European Journal of Cell Biology
https://www.readbyqxmd.com/read/27911821/myth4-ferm-myosins-have-an-ancient-and-conserved-role-in-filopod-formation
#4
Karl J Petersen, Holly V Goodson, Ashley L Arthur, G W Gant Luxton, Anne Houdusse, Margaret A Titus
The formation of filopodia in Metazoa and Amoebozoa requires the activity of myosin 10 (Myo10) in mammalian cells and of Dictyostelium unconventional myosin 7 (DdMyo7) in the social amoeba Dictyostelium However, the exact roles of these MyTH4-FERM myosins (myosin tail homology 4-band 4.1, ezrin, radixin, moesin; MF) in the initiation and elongation of filopodia are not well defined and may reflect conserved functions among phylogenetically diverse MF myosins. Phylogenetic analysis of MF myosin domains suggests that a single ancestral MF myosin existed with a structure similar to DdMyo7, which has two MF domains, and that subsequent duplications in the metazoan lineage produced its functional homolog Myo10...
November 23, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27881166/using-the-social-amoeba-dictyostelium-to-study-the-functions-of-proteins-linked-to-neuronal-ceroid-lipofuscinosis
#5
REVIEW
Robert J Huber
Neuronal ceroid lipofuscinosis (NCL), also known as Batten disease, is a debilitating neurological disorder that affects both children and adults. Thirteen genetically distinct genes have been identified that when mutated, result in abnormal lysosomal function and an excessive accumulation of ceroid lipofuscin in neurons, as well as other cell types outside of the central nervous system. The NCL family of proteins is comprised of lysosomal enzymes (PPT1/CLN1, TPP1/CLN2, CTSD/CLN10, CTSF/CLN13), proteins that peripherally associate with membranes (DNAJC5/CLN4, KCTD7/CLN14), a soluble lysosomal protein (CLN5), a protein present in the secretory pathway (PGRN/CLN11), and several proteins that display different subcellular localizations (CLN3, CLN6, MFSD8/CLN7, CLN8, ATP13A2/CLN12)...
November 24, 2016: Journal of Biomedical Science
https://www.readbyqxmd.com/read/27872153/xpf-suppresses-mutagenic-consequences-of-bacterial-phagocytosis-in-dictyostelium
#6
Lucas B Pontel, Judith Langenick, Ivan V Rosado, Xiao-Yin Zhang, David Traynor, Robert R Kay, Ketan J Patel
As time passes, mutations accumulate in the genomes of all living organisms. These changes promote genetic diversity, but also precipitate ageing and the initiation of cancer. Food is a common source of mutagens, but little is known about how nutritional factors cause lasting genetic changes in the consuming organism. Here, we describe an unusual genetic interaction between DNA repair in the unicellular amoeba - Dictyostelium discoideum - and its natural bacterial food source. Dictyostelium deficient in the DNA repair nuclease Xpf displays a severe and specific growth defect when feeding on bacteria...
November 21, 2016: Journal of Cell Science
https://www.readbyqxmd.com/read/27862766/terpene-cyclases-from-social-amoebae
#7
Patrick Rabe, Jan Rinkel, Britta Nubbemeyer, Tobias G Köllner, Feng Chen, Jeroen S Dickschat
Genome sequences of social amoebae reveal the presence of terpene cyclases (TCs) in these organisms. Two TCs from Dictyostelium discoideum converted farnesyl diphosphate into (2S,3R,6S,9S)-(-)-protoillud-7-ene and (3S)-(+)-asterisca-2(9),6-diene. The enzyme mechanisms and EI-MS fragmentations of the products were studied by labeling experiments.
November 10, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27855631/a-core-phylogeny-of-dictyostelia-inferred-from-genomes-representative-of-the-eight-major-and-minor-taxonomic-divisions-of-the-group
#8
Reema Singh, Christina Schilde, Pauline Schaap
BACKGROUND: Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa...
November 17, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27836548/functional-characterisation-of-parvulin-type-peptidyl-prolyl-cis-trans-isomerase-pina-in-dictyostelium-discoideum
#9
Nemneineng Haokip, Aruna Naorem
Pin1-type parvulins are unique among PPIases that can catalyse an otherwise slow cis-trans isomerisation of phosphorylated peptide bond preceding proline in target proteins. This prolyl isomerisation process can regulate activity, stability and localisation of target proteins and thus control cellular processes like eukaryotic cell proliferation, cell cycle progression and gene regulation. Towards understanding the function of Pin1-type prolyl isomerisation in Dictyostelium discoideum, a slime mould with distinct growth and developmental phases, we identified PinA as a novel Pin1-type parvulin by its ability to complement the temperature sensitivity phenotype associated with a mutation in ESS1 in S...
November 9, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27821733/a-diaphanous-related-formin-links-ras-signaling-directly-to-actin-assembly-in-macropinocytosis-and-phagocytosis
#10
Alexander Junemann, Vedrana Filić, Moritz Winterhoff, Benjamin Nordholz, Christof Litschko, Helena Schwellenbach, Till Stephan, Igor Weber, Jan Faix
Phagocytosis and macropinocytosis are Ras-regulated and actin-driven processes that depend on the dynamic rearrangements of the plasma membrane that protrudes and internalizes extracellular material by cup-shaped structures. However, the regulatory mechanisms underlying actin assembly in large-scale endocytosis remain elusive. Here, we show that the Diaphanous-related formin G (ForG) from the professional phagocyte Dictyostelium discoideum localizes to endocytic cups. Biochemical analyses revealed that ForG is a rather weak nucleator but efficiently elongates actin filaments in the presence of profilin...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27818653/dictyostelium-discoideum-as-a-novel-host-system-to-study-the-interaction-between-phagocytes-and-yeasts
#11
Barbara Koller, Christin Schramm, Susann Siebert, János Triebel, Eric Deland, Anna M Pfefferkorn, Volker Rickerts, Sascha Thewes
The social amoeba Dictyostelium discoideum is a well-established model organism to study the interaction between bacteria and phagocytes. In contrast, research using D. discoideum as a host model for fungi is rare. We describe a comprehensive study, which uses D. discoideum as a host model system to investigate the interaction with apathogenic (Saccharomyces cerevisiae) and pathogenic (Candida sp.) yeast. We show that Dictyostelium can be co-cultivated with yeasts on solid media, offering a convenient test to study the interaction between fungi and phagocytes...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27814692/a-set-of-genes-conserved-in-sequence-and-expression-traces-back-the-establishment-of-multicellularity-in-social-amoebae
#12
Christina Schilde, Hajara M Lawal, Angelika A Noegel, Ludwig Eichinger, Pauline Schaap, Gernot Glöckner
BACKGROUND: The developmental cycle of Dictyostelid amoebae represents an early form of multicellularity with cell type differentiation. Mutant studies in the model Dictyostelium discoideum revealed that its developmental program integrates the actions of genes involved in signal transduction, adhesion, motility, autophagy and cell wall and matrix biosynthesis. However, due to functional redundancy and fail safe options not required in the laboratory, this single organism approach cannot capture all essential genes...
November 4, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27798280/inference-of-the-drivers-of-collective-movement-in-two-cell-types-dictyostelium-and-melanoma
#13
Elaine A Ferguson, Jason Matthiopoulos, Robert H Insall, Dirk Husmeier
Collective cell movement is a key component of many important biological processes, including wound healing, the immune response and the spread of cancers. To understand and influence these movements, we need to be able to identify and quantify the contribution of their different underlying mechanisms. Here, we define a set of six candidate models-formulated as advection-diffusion-reaction partial differential equations-that incorporate a range of cell movement drivers. We fitted these models to movement assay data from two different cell types: Dictyostelium discoideum and human melanoma...
October 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/27791032/v-1-regulates-capping-protein-activity-in-vivo
#14
Goeh Jung, Christopher J Alexander, Xufeng S Wu, Grzegorz Piszczek, Bi-Chang Chen, Eric Betzig, John A Hammer
Capping Protein (CP) plays a central role in the creation of the Arp2/3-generated branched actin networks comprising lamellipodia and pseudopodia by virtue of its ability to cap the actin filament barbed end, which promotes Arp2/3-dependent filament nucleation and optimal branching. The highly conserved protein V-1/Myotrophin binds CP tightly in vitro to render it incapable of binding the barbed end. Here we addressed the physiological significance of this CP antagonist in Dictyostelium, which expresses a V-1 homolog that we show is very similar biochemically to mouse V-1...
October 25, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27790999/terpene-synthase-genes-in-eukaryotes-beyond-plants-and-fungi-occurrence-in-social-amoebae
#15
Xinlu Chen, Tobias G Köllner, Qidong Jia, Ayla Norris, Balaji Santhanam, Patrick Rabe, Jeroen S Dickschat, Gad Shaulsky, Jonathan Gershenzon, Feng Chen
Terpenes are structurally diverse natural products involved in many ecological interactions. The pivotal enzymes for terpene biosynthesis, terpene synthases (TPSs), had been described only in plants and fungi in the eukaryotic domain. In this report, we systematically analyzed the genome sequences of a broad range of nonplant/nonfungus eukaryotes and identified putative TPS genes in six species of amoebae, five of which are multicellular social amoebae from the order of Dictyosteliida. A phylogenetic analysis revealed that amoebal TPSs are evolutionarily more closely related to fungal TPSs than to bacterial TPSs...
October 25, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27737633/huntingtin-associated-protein-1-eutherian-adaptation-from-a%C3%A2-trak-like-protein-conserved-gene-promoter-elements-and-localization-in-the-human-intestine
#16
Amanda L Lumsden, Richard L Young, Nektaria Pezos, Damien J Keating
BACKGROUND: Huntingtin-associated Protein 1 (HAP1) is expressed in neurons and endocrine cells, and is critical for postnatal survival in mice. HAP1 shares a conserved "HAP1_N" domain with TRAfficking Kinesin proteins TRAK1 and TRAK2 (vertebrate), Milton (Drosophila) and T27A3.1 (C. elegans). HAP1, TRAK1 and TRAK2 have a degree of common function, particularly regarding intracellular receptor trafficking. However, TRAK1, TRAK2 and Milton (which have a "Milt/TRAK" domain that is absent in human and rodent HAP1) differ in function to HAP1 in that they are mitochondrial transport proteins, while HAP1 has emerging roles in starvation response...
October 13, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27735954/the-microfluidic-lighthouse-an-omnidirectional-gradient-generator
#17
A Nakajima, M Ishida, T Fujimori, Y Wakamoto, S Sawai
Studies of chemotactic cell migration rely heavily on various assay systems designed to evaluate the ability of cells to move in response to attractant molecules. In particular, the development of microfluidics-based devices in recent years has made it possible to spatially distribute attractant molecules in graded profiles that are sufficiently stable and precise to test theoretical predictions regarding the accuracy and efficiency of chemotaxis and the underlying mechanism of stimulus perception. However, because the gradient is fixed in a direction orthogonal to the laminar flow and thus the chamber geometry, conventional devices are limited for the study of cell re-orientation to gradients that move or change directions...
October 13, 2016: Lab on a Chip
https://www.readbyqxmd.com/read/27715492/connecting-g-protein-signaling-to-chemoattractant-mediated-cell-polarity-and-cytoskeletal-reorganization
#18
Youtao Liu, Jesus Lacal, Richard A Firtel, Arjan Kortholt
The directional movement towards extracellular chemical gradients, a process called chemotaxis, is an important property of cells. Central to eukaryotic chemotaxis is the molecular mechanism by which chemoattractant-mediated activation of G-protein coupled receptors (GPCRs) induces symmetry breaking in the activated downstream signaling pathways. Studies with mainly Dictyostelium and mammalian neutrophils as experimental systems have shown that chemotaxis is mediated by a complex network of signaling pathways...
October 7, 2016: Small GTPases
https://www.readbyqxmd.com/read/27715405/autophagy-in-dictyostelium-mechanisms-regulation-and-disease-in-a-simple-biomedical-model
#19
Ana Mesquita, Elena Cardenal-Muñoz, Eunice Dominguez, Sandra Muñoz-Braceras, Beatriz Nuñez-Corcuera, Ben A Phillips, Luis C Tábara, Qiuhong Xiong, Roberto Coria, Ludwig Eichinger, Pierre Golstein, Jason S King, Thierry Soldati, Olivier Vincent, Ricardo Escalante
Autophagy is a fast-moving field with an enormous impact on human health and disease. Understanding the complexity of the mechanism and regulation of this process often benefits from the use of simple experimental models such as the social amoeba Dictyostelium discoideum. Since the publication of the first review describing the potential of D. discoideum in autophagy, significant advances have been made that demonstrate both the experimental advantages and interest in using this model. Since our previous review, research in D...
October 7, 2016: Autophagy
https://www.readbyqxmd.com/read/27708767/progress-and-perspectives-in-signal-transduction-actin-dynamics-and-movement-at-the-cell-and-tissue-level-lessons-from-dictyostelium
#20
REVIEW
Till Bretschneider, Hans G Othmer, Cornelis J Weijer
Movement of cells and tissues is a basic biological process that is used in development, wound repair, the immune response to bacterial invasion, tumour formation and metastasis, and the search for food and mates. While some cell movement is random, directed movement stimulated by extracellular signals is our focus here. This involves a sequence of steps in which cells first detect extracellular chemical and/or mechanical signals via membrane receptors that activate signal transduction cascades and produce intracellular signals...
October 6, 2016: Interface Focus
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