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Mobile genome element

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https://www.readbyqxmd.com/read/27902415/inversion-of-correia-repeat-enclosed-elements-in-neisseria-gonorrhoeae
#1
Firat Elbeyioglu, Sabrina B Roberts, Russell Spencer-Smith, Madhuri Pulijala, Marta A Zelewska, Jean-Christophe Nebel, Lori As Snyder
Neisseria gonorrhoeae is capable of causing gonorrhoea and more complex diseases in the human host. Within the gonococcal genome are over 100 copies of the IS-like Correia Repeat Enclosed Element, which has been predicted to be mobile within the neisserial genomes. Although there is evidence of ancestral movement of these elements, no previous study has provided evidence for current mobilisation. The Correia Repeat Enclosed Element has the ability to alter gene expression and regulation in many ways: by insertional mutagenesis; by introducing promoter elements; by generating mRNA processing sites, and by association with ncRNAs...
November 16, 2016: Microbiology
https://www.readbyqxmd.com/read/27899587/temporal-self-regulation-of-transposition-through-host-independent-transposase-rodlet-formation
#2
Lauren E Woodard, Laura M Downes, Yi-Chien Lee, Aparna Kaja, Eyuel S Terefe, Matthew H Wilson
Transposons are highly abundant in eukaryotic genomes, but their mobilization must be finely tuned to maintain host organism fitness and allow for transposon propagation. Forty percent of the human genome is comprised of transposable element sequences, and the most abundant cut-and-paste transposons are from the hAT superfamily. We found that the hAT transposase TcBuster from Tribolium castaneum formed filamentous structures, or rodlets, in human tissue culture cells, after gene transfer to adult mice, and ex vivo in cell-free conditions, indicating that host co-factors or cellular structures were not required for rodlet formation...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899566/asymmetric-positioning-of-cas1-2-complex-and-integration-host-factor-induced-dna-bending-guide-the-unidirectional-homing-of-protospacer-in-crispr-cas-type-i-e-system
#3
K N R Yoganand, R Sivathanu, Siddharth Nimkar, B Anand
CRISPR-Cas system epitomizes prokaryote-specific quintessential adaptive defense machinery that limits the genome invasion of mobile genetic elements. It confers adaptive immunity to bacteria by capturing a protospacer fragment from invading foreign DNA, which is later inserted into the leader proximal end of CRIPSR array and serves as immunological memory to recognize recurrent invasions. The universally conserved Cas1 and Cas2 form an integration complex that is known to mediate the protospacer invasion into the CRISPR array...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27895722/deciphering-fact-from-artifact-when-using-reporter-assays-to-investigate-the-roles-of-host-factors-on-l1-retrotransposition
#4
Pamela R Cook, G Travis Tabor
BACKGROUND: The Long INterspersed Element-1 (L1, LINE-1) is the only autonomous mobile DNA element in humans and has generated as much as half of the genome. Due to increasing clinical interest in the roles of L1 in cancer, embryogenesis and neuronal development, it has become a priority to understand L1-host interactions and identify host factors required for its activity. Apropos to this, we recently reported that L1 retrotransposition in HeLa cells requires phosphorylation of the L1 protein ORF1p at motifs targeted by host cell proline-directed protein kinases (PDPKs), which include the family of mitogen-activated protein kinases (MAPKs)...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27892853/structure-of-the-germline-genome-of-tetrahymenathermophila-and-relationship-to-the-massively-rearranged-somatic-genome
#5
Eileen P Hamilton, Aurélie Kapusta, Piroska E Huvos, Shelby L Bidwell, Nikhat Zafar, Haibao Tang, Michalis Hadjithomas, Vivek Krishnakumar, Jonathan H Badger, Elisabet V Caler, Carsten Russ, Qiandong Zeng, Lin Fan, Joshua Z Levin, Terrance Shea, Sarah K Young, Ryan Hegarty, Riza Daza, Sharvari Gujja, Jennifer R Wortman, Bruce W Birren, Chad Nusbaum, Jainy Thomas, Clayton M Carey, Ellen J Pritham, Cédric Feschotte, Tomoko Noto, Kazufumi Mochizuki, Romeo Papazyan, Sean D Taverna, Paul H Dear, Donna M Cassidy-Hanley, Jie Xiong, Wei Miao, Eduardo Orias, Robert S Coyne
The germline genome of the binucleated ciliate Tetrahymenathermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally...
November 28, 2016: ELife
https://www.readbyqxmd.com/read/27886494/stochastic-predator-prey-dynamics-of-transposons-in-the-human-genome
#6
Chi Xue, Nigel Goldenfeld
Transposable elements, or transposons, are DNA sequences that can jump from site to site in the genome during the life cycle of a cell, usually encoding the very enzymes which perform their excision. However, some transposons are parasitic, relying on the enzymes produced by the regular transposons. In this case, we show that a stochastic model, which takes into account the small copy numbers of the active transposons in a cell, predicts noise-induced predator-prey oscillations with a characteristic time scale that is much longer than the cell replication time, indicating that the state of the predator-prey oscillator is stored in the genome and transmitted to successive generations...
November 11, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27880983/pantoea-ananatis-genomic-insights-into-a-versatile-pathogen
#7
Tania Weller-Stuart, Pieter De Maayer, Teresa Coutinho
Pantoea ananatis, a bacterium that is well-known for its phytopathogenic characteristics, has been isolated from a myriad of ecological niches and hosts. Infection of agronomic crops such as maize and rice can result in substantial economic losses. In the last few years, much of the research done on P. ananatis has been based on the sequencing and analysis of the genomes of strains isolated from different environments and with different lifestyles. In this review we summarise the advances made in terms of pathogenicity determinants of phytopathogenic strains of P...
November 23, 2016: Molecular Plant Pathology
https://www.readbyqxmd.com/read/27875251/the-impact-of-transposable-elements-on-mammalian-development
#8
REVIEW
Jose L Garcia-Perez, Thomas J Widmann, Ian R Adams
Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that have a significant impact on mammalian development and genome regulation. In recent years, our understanding of how pre-existing TEs affect genome architecture, gene regulatory networks and protein function during mammalian embryogenesis has dramatically expanded. In addition, the mobilization of active TEs in selected cell types has been shown to generate genetic variation during development and in fully differentiated tissues...
November 15, 2016: Development
https://www.readbyqxmd.com/read/27869745/many-activities-one-structure-functional-plasticity-of-ribozyme-folds
#9
REVIEW
Matthew W L Lau, Adrian R Ferré-D'Amaré
Catalytic RNAs, or ribozymes, are involved in a number of essential biological processes, such as replication of RNA genomes and mobile genetic elements, RNA splicing, translation, and RNA degradation. The function of ribozymes requires the formation of active sites decorated with RNA functional groups within defined three-dimensional (3D) structures. The genotype (sequence) of RNAs ultimately determines what 3D structures they adopt (as a function of their environmental conditions). These 3D structures, in turn, give rise to biochemical activity, which can further elaborate them by catalytic rearrangements or association with other molecules...
November 18, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27869532/molecular-characterization-of-methicillin-resistant-staphylococcus-aureus-from-outpatients-in-northern-japan-increasing-tendency-of-st5-st764-mrsa-iia-with-arginine-catabolic-mobile-element
#10
Meiji Soe Aung, Mitsuyo Kawaguchiya, Noriko Urushibara, Ayako Sumi, Masahiko Ito, Kenji Kudo, Shigeo Morimoto, Shino Hosoya, Nobumichi Kobayashi
Arginine catabolic mobile element (ACME) is a genomic island of staphylococcus and is considered to confer enhanced ability to survive and growth on host bacterial cells. ACME has been typically identified in Panton-Valentine Leukocidin (PVL)-positive ST8 methicillin-resistant Staphylococcus aureus (MRSA) with SCCmec type IVa (USA300 clone), and it is also found in other lineages at low frequency. Prevalence and molecular characteristics of PVL(+)and/or ACME(+) MRSA were investigated for 624 clinical isolates collected from outpatients in northern Japan from 2013 to 2014...
November 21, 2016: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/27863519/tet-dependent-regulation-of-retrotransposable-elements-in-mouse-embryonic-stem-cells
#11
Lorenzo de la Rica, Özgen Deniz, Kevin C L Cheng, Christopher D Todd, Cristina Cruz, Jonathan Houseley, Miguel R Branco
BACKGROUND: Ten-eleven translocation (TET) enzymes oxidise DNA methylation as part of an active demethylation pathway. Despite extensive research into the role of TETs in genome regulation, little is known about their effect on transposable elements (TEs), which make up nearly half of the mouse and human genomes. Epigenetic mechanisms controlling TEs have the potential to affect their mobility and to drive the co-adoption of TEs for the benefit of the host. RESULTS: We performed a detailed investigation of the role of TET enzymes in the regulation of TEs in mouse embryonic stem cells (ESCs)...
November 18, 2016: Genome Biology
https://www.readbyqxmd.com/read/27849579/plant-nodulation-inducers-enhance-horizontal-gene-transfer-of-azorhizobium-caulinodans-symbiosis-island
#12
Jun Ling, Hui Wang, Ping Wu, Tao Li, Yu Tang, Nawar Naseer, Huiming Zheng, Catherine Masson-Boivin, Zengtao Zhong, Jun Zhu
Horizontal gene transfer (HGT) of genomic islands is a driving force of bacterial evolution. Many pathogens and symbionts use this mechanism to spread mobile genetic elements that carry genes important for interaction with their eukaryotic hosts. However, the role of the host in this process remains unclear. Here, we show that plant compounds inducing the nodulation process in the rhizobium-legume mutualistic symbiosis also enhance the transfer of symbiosis islands. We demonstrate that the symbiosis island of the Sesbania rostrata symbiont, Azorhizobium caulinodans, is an 87...
November 14, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27845364/a-genomic-island-in-vibrio-cholerae-with-vpi-1-site-specific-recombination-characteristics-contains-crispr-cas-and-type-vi-secretion-modules
#13
Maurizio Labbate, Fabini D Orata, Nicola K Petty, Nathasha D Jayatilleke, William L King, Paul C Kirchberger, Chris Allen, Gulay Mann, Ankur Mutreja, Nicholas R Thomson, Yan Boucher, Ian G Charles
Cholera is a devastating diarrhoeal disease caused by certain strains of serogroup O1/O139 Vibrio cholerae. Mobile genetic elements such as genomic islands (GIs) have been pivotal in the evolution of O1/O139 V. cholerae. Perhaps the most important GI involved in cholera disease is the V. cholerae pathogenicity island 1 (VPI-1). This GI contains the toxin-coregulated pilus (TCP) gene cluster that is necessary for colonization of the human intestine as well as being the receptor for infection by the cholera-toxin bearing CTX phage...
November 15, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27826290/draft-genomic-analysis-of-an-avian-multidrug-resistant-morganella-morganii-isolate-carrying-qnrd1
#14
Daniela Jones-Dias, Lurdes Clemente, Inês B Moura, Daniel A Sampaio, Teresa Albuquerque, Luís Vieira, Vera Manageiro, Manuela Caniça
Morganella morganii is a commensal bacterium and opportunistic pathogen often present in the gut of humans and animals. We report the 4.3 Mbp draft genome sequence of a M. morganii isolated in association with an Escherichia coli from broilers in Portugal that showed macroscopic lesions consistent with colisepticemia. The analysis of the genome matched the multidrug resistance phenotype and enabled the identification of several clinically important and potentially mobile acquired antibiotic resistance genes, including the plasmid-mediated quinolone resistance determinant qnrD1...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27821059/recent-and-dynamic-transposable-elements-contribute-to-genomic-divergence-under-asexuality
#15
Julie Ferreira de Carvalho, Victor de Jager, Thomas P van Gurp, Niels C A M Wagemaker, Koen J F Verhoeven
BACKGROUND: Transposable elements (TEs) are mobile pieces of genetic information with high mutagenic potential for the host genome. Transposition is often neutral or deleterious but may also generate potentially adaptive genetic variation. This additional source of variation could be especially relevant in non-recombining species reproducing asexually. However, evidence is lacking to determine the relevance of TEs in plant asexual genome evolution and their associated effects. Here, we characterize the repetitive fraction of the genome of the common dandelion, Taraxacum officinale and compare it between five accessions from the same apomictic lineage...
November 7, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27812409/the-mosaic-architecture-of-aeromonas-salmonicida-subsp-salmonicida-pasa4-plasmid-and-its-consequences-on-antibiotic-resistance
#16
Katherine H Tanaka, Antony T Vincent, Mélanie V Trudel, Valérie E Paquet, Michel Frenette, Steve J Charette
Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis in salmonids, is an issue especially because many isolates of this bacterium display antibiotic resistances, which limit treatments against the disease. Recent results suggested the possible existence of alternative forms of pAsa4, a large plasmid found in A. salmonicida subsp. salmonicida and bearing multiple antibiotic resistance genes. The present study reveals the existence of two newly detected pAsa4 variants, pAsa4b and pAsa4c...
2016: PeerJ
https://www.readbyqxmd.com/read/27807467/a-map-of-mobile-dna-insertions-in-the-nci-60-human-cancer-cell-panel
#17
John G Zampella, Nemanja Rodić, Wan Rou Yang, Cheng Ran Lisa Huang, Jane Welch, Veena P Gnanakkan, Toby C Cornish, Jef D Boeke, Kathleen H Burns
BACKGROUND: The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expression, and pharmacologic susceptibilities in studies of cancer cell biology. Genome-wide studies of the complete panel have included exome sequencing, karyotyping, and copy number analyses but have not targeted repetitive sequences. Interspersed repeats derived from mobile DNAs are a significant source of heritable genetic variation, and insertions of active elements can occur somatically in malignancy...
2016: Mobile DNA
https://www.readbyqxmd.com/read/27799520/drosophila-irbp-bzip-heterodimer-binds-p-element-dna-and-affects-hybrid-dysgenesis
#18
Malik Joseph Francis, Siobhan Roche, Michael Jeffrey Cho, Eileen Beall, Bosun Min, Ronaldo Paolo Panganiban, Donald C Rio
In Drosophila, P-element transposition causes mutagenesis and genome instability during hybrid dysgenesis. The P-element 31-bp terminal inverted repeats (TIRs) contain sequences essential for transposase cleavage and have been implicated in DNA repair via protein-DNA interactions with cellular proteins. The identity and function of these cellular proteins were unknown. Biochemical characterization of proteins that bind the TIRs identified a heterodimeric basic leucine zipper (bZIP) complex between an uncharacterized protein that we termed "Inverted Repeat Binding Protein (IRBP) 18" and its partner Xrp1...
October 31, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27799346/pirnas-and-their-diverse-roles-a-transposable-element-driven-tactic-for-gene-regulation
#19
REVIEW
Arpita Sarkar, Jean-Nicolas Volff, Chantal Vaury
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are small, noncoding RNAs known for silencing transposable elements (TEs) in the germline of animals. Most genomes host TEs, which are notorious for mobilizing themselves and endangering survival of the host if not controlled. By silencing TEs in the germline, piRNAs prevent harmful mutations from being passed on to the next generation. How piRNAs are generated and how they silence TEs were the focus of researchers ever since their discovery. Now a spate of recent papers are beginning to tell us that piRNAs can play roles beyond TE silencing and are involved in diverse cellular processes from mRNA regulation to development or genome rearrangement...
October 31, 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/27795287/genomic-evolution-of-two-acinetobacter-baumannii-clinical-strains-from-st-2-clones-isolated-in-2000-and-2010-st-2_clon_2000-and-st-2_clon_2010
#20
M López, A Rueda, J P Florido, L Blasco, E Gato, L Fernández-García, L Martínez-Martínez, F Fernández-Cuenca, J Pachón, J M Cisneros, J Garnacho-Montero, J Vila, J Rodríguez-Baño, A Pascual, G Bou, M Tomás
Acinetobacter baumannii is a successful nosocomial pathogen due to its ability to persist in hospital environments by acquiring mobile elements such as transposons, plasmids, and phages. In this study, we compared two genomes of A. baumannii clinical strains isolated in 2000 (ST-2_clon_2000) and 2010 (ST-2_clon_2010) from GenBank project PRJNA308422.
October 20, 2016: Genome Announcements
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