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Mobile genetic element

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https://www.readbyqxmd.com/read/29165361/the-obscure-world-of-integrative-and-mobilizable-elements-highly-widespread-elements-that-pirate-bacterial-conjugative-systems
#1
REVIEW
Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot, Nathalie Leblond-Bourget
Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. Recent findings indicated that the main actors of conjugative transfer are not the well-known conjugative or mobilizable plasmids but are the integrated elements. This paper reviews current knowledge on "integrative and mobilizable elements" (IMEs) that have recently been shown to be highly diverse and highly widespread but are still rarely described. IMEs encode their own excision and integration and use the conjugation machinery of unrelated co-resident conjugative element for their own transfer...
November 22, 2017: Genes
https://www.readbyqxmd.com/read/29163390/comparative-genomics-reveals-specific-genetic-architectures-in-nicotine-metabolism-of-pseudomonas-sp-jy-q
#2
Jun Li, Shulan Qian, Lie Xiong, Chengyun Zhu, Ming Shu, Jie Wang, Yang Jiao, Houlong He, Fuming Zhang, Robert J Linhardt, Weihong Zhong
Microbial degradation of nicotine is an important process to control nicotine residues in the aqueous environment. In this study, a high active nicotine degradation strain named Pseudomonas sp. JY-Q was isolated from tobacco waste extract (TWE). This strain could completely degrade 5.0 g l(-1) nicotine in 24 h under optimal culture conditions, and it showed some tolerance even at higher concentrations (10.0 g l(-1)) of nicotine. The complete genome of JY-Q was sequenced to understand the mechanism by which JY-Q could degrade nicotine and tolerate such high nicotine concentrations...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163120/the-myosuit-bi-articular-anti-gravity-exosuit-that-reduces-hip-extensor-activity-in-sitting-transfers
#3
Kai Schmidt, Jaime E Duarte, Martin Grimmer, Alejandro Sancho-Puchades, Haiqi Wei, Chris S Easthope, Robert Riener
Muscle weakness-which can result from neurological injuries, genetic disorders, or typical aging-can affect a person's mobility and quality of life. For many people with muscle weakness, assistive devices provide the means to regain mobility and independence. These devices range from well-established technology, such as wheelchairs, to newer technologies, such as exoskeletons and exosuits. For assistive devices to be used in everyday life, they must provide assistance across activities of daily living (ADLs) in an unobtrusive manner...
2017: Frontiers in Neurorobotics
https://www.readbyqxmd.com/read/29160003/two-new-viruses-mcv1-and-mcv2-which-infect-marinitoga-bacteria-isolated-from-deep-sea-hydrothermal-vents-functional-and-genomic-analysis
#4
C Mercier, J Lossouarn, C L Nesbø, T H A Haverkamp, A C Baudoux, M Jebbar, N Bienvenu, S Thiroux, S Dupont, C Geslin
Viruses represent a driving force in the evolution of microorganisms including those thriving in extreme environments. However, our knowledge of the viral diversity associated to microorganisms inhabiting the deep-sea hydrothermal vents remains limited. The phylum of Thermotogae, including thermophilic bacteria, is well represented in this environment. Only one virus was described in this phylum, MPV1 carried by Marinitoga piezophila. In this study, we report on the functional and genomic characterization of two new bacterioviruses that infect bacteria from the Marinitoga genus...
November 21, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29155231/rtfadb-a-database-of-computationally-predicted-associations-between-retrotransposons-and-transcription-factors-in-the-human-and-mouse-genomes
#5
Gökhan Karakülah
In recent years, retrotransposons have gained increasing attention as a source of binding motifs for transcription factors (TFs). Despite the substantial roles of these mobile genetic elements in the regulation of gene expression, a comprehensive resource enabling the investigation of retrotransposon species that are bound by TFs is still lacking. Herein, I introduce for the first time a novel database called RTFAdb, which allows exploring computationally predicted associations between retrotransposons and TFs in diverse cell lines and tissues of human and mouse...
November 16, 2017: Genomics
https://www.readbyqxmd.com/read/29154097/diversity-abundance-and-persistence-of-antibiotic-resistance-genes-in-various-types-of-animal-manure-following-industrial-composting
#6
Xun Qian, Jie Gu, Wei Sun, Xiao-Juan Wang, Jian-Qiang Su, Robert Stedfeld
Aerobic composting is used widely for animal manure recycling, and it may reduce the amount of antibiotic resistance genes (ARGs) that enter the environment. We sampled three types of animal (bovine, chicken, and pig) manure and the corresponding composts from 12 large-scale farms, and tested multiple ARGs and mobile genetic elements (MGEs) by high-throughput qPCR. A total of 109 ARGs were detected in the manure and compost samples, thereby demonstrating that both are important ARG reservoirs. The diversity and abundance of ARGs were significantly higher in chicken and pig manure than bovine manure, but industrial composting was more efficient at reducing the ARGs in chicken manure than pig and bovine manure...
November 13, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/29152580/chromosomal-targeting-by-the-type-iii-a-crispr-cas-system-can-reshape-genomes-in-staphylococcus-aureus
#7
Jing Guan, Wanying Wang, Baolin Sun
CRISPR-Cas (clustered regularly interspaced short palindromic repeat [CRISPR]-CRISPR-associated protein [Cas]) systems can provide protection against invading genetic elements by using CRISPR RNAs (crRNAs) as a guide to locate and degrade the target DNA. CRISPR-Cas systems have been classified into two classes and five types according to the content of cas genes. Previous studies have indicated that CRISPR-Cas systems can avoid viral infection and block plasmid transfer. Here we show that chromosomal targeting by the Staphylococcus aureus type III-A CRISPR-Cas system can drive large-scale genome deletion and alteration within integrated staphylococcal cassette chromosome mec (SCCmec)...
November 2017: MSphere
https://www.readbyqxmd.com/read/29150513/high-prevalence-and-genetic-diversity-of-large-phicd211-phicdif1296t-like-prophages-in-clostridioides-difficile
#8
Julian R Garneau, Ognjen Sekulovic, Bruno Dupuy, Olga Soutourina, Marc Monot, Louis-Charles Fortier
Clostridioides difficile (formerly Clostridium difficile) is a pathogenic bacterium displaying great genetic diversity. A significant proportion of this diversity is due to the presence of integrated prophages. Here, we provide an in-depth analysis of phiCD211, also known as phiCDIF1296T, the largest phage identified in C. difficile so far, with a genome of 131-kbp. It shares morphological and genomic similarity with other large siphophages like phage 949 infecting Lactococcus lactis and phage c-st infecting Clostridium botulinum...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29145853/molecular-characterization-of-%C3%AE-lactamase-genes-in-clinical-isolates-of-carbapenem-resistant-acinetobacter-baumannii
#9
Kevin M Raible, Bhaswati Sen, Nancy Law, Tiffany E Bias, Christopher L Emery, Garth D Ehrlich, Suresh G Joshi
BACKGROUND: Acinetobacter baumannii is a nosocomial pathogen which is establishing as a major cause of morbidity and mortality within the healthcare community. The success of this pathogen is largely due to its ability to rapidly gain resistance to antimicrobial therapies and its capability to persist in an abiotic environment through the production of a biofilm. Our tertiary-care hospital has showed high incidence of carbapenem-resistant Acinetobacter baumannii (CRAB) isolates. METHODS: In this study we explore both genotypic and phenotypic properties of 26 CRAB isolates: 16 isolates were collected from January 2010 to March 2011, and 10 were collected between February and May 2015...
November 16, 2017: Annals of Clinical Microbiology and Antimicrobials
https://www.readbyqxmd.com/read/29134601/transposable-bacteriophages-as-genetic-tools
#10
Ariane Toussaint
Phage Mu is the paradigm of a growing family of bacteriophages that infect a wide range of bacterial species and replicate their genome by replicative transposition. This molecular process, which is used by other mobile genetic elements to move within genomes, involves the profound rearrangement of the host genome [chromosome(s) and plasmid(s)] and can be exploited for the genetic analysis of the host bacteria and the in vivo cloning of host genes. In this chapter we review Mu-derived constructs that optimize the phage as a series of genetic tools that could inspire the development of similarly efficient tools from other transposable phages for a large spectrum of bacteria...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29133551/copper-ions-and-coordination-complexes-as-novel-carbapenem-adjuvants
#11
Karrera Y Djoko, Maud E S Achard, Minh-Duy Phan, Alvin W Lo, Manfredi Miraula, Sasiprapa Prombhul, Steven J Hancock, Kate M Peters, Hanna Sidjabat, Patrick N Harris, Nataša Mitić, Timothy R Walsh, Gregory J Anderson, William M Shafer, David L Paterson, Gerhard Schenk, Alastair G McEwan, Mark A Schembri
Carbapenem-resistant Enterobacteriaceae are an urgent threat to global human health. These organisms produce β-lactamases with carbapenemase activity, such as the metallo-β-lactamase NDM-1, which is notable due to its association with mobile genetic elements and the lack of a clinically useful inhibitor. Here we examined the ability of copper to inhibit the activity of NDM-1 and explored the potential of a copper coordination complex as a mechanism to efficiently deliver copper as an adjuvant in clinical therapeutics...
November 13, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29127343/global-phylogenetic-analysis-of-escherichia-coli-and-plasmids-carrying-the-mcr-1-gene-indicates-bacterial-diversity-but-plasmid-restriction
#12
Sébastien Matamoros, Jarne M van Hattem, Maris S Arcilla, Niels Willemse, Damian C Melles, John Penders, Trung Nguyen Vinh, Ngo Thi Hoa, Menno D de Jong, Constance Schultsz
To understand the dynamics behind the worldwide spread of the mcr-1 gene, we determined the population structure of Escherichia coli and of mobile genetic elements (MGEs) carrying the mcr-1 gene. After a systematic review of the literature we included 65 E. coli whole genome sequences (WGS), adding 6 recently sequenced travel related isolates, and 312 MLST profiles. We included 219 MGEs described in 7 Enterobacteriaceae species isolated from human, animal and environmental samples. Despite a high overall diversity, 2 lineages were observed in the E...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29126393/genomic-characterisation-of-clinical-and-environmental-pseudomonas-putida-group-strains-and-determination-of-their-role-in-the-transfer-of-antimicrobial-resistance-genes-to-pseudomonas-aeruginosa
#13
Silke Peter, Philipp Oberhettinger, Leonard Schuele, Ariane Dinkelacker, Wichard Vogel, Daniela Dörfel, Daniela Bezdan, Stephan Ossowski, Matthias Marschal, Jan Liese, Matthias Willmann
BACKGROUND: Pseudomonas putida is a Gram-negative, non-fermenting bacterium frequently encountered in various environmental niches. P. putida rarely causes disease in humans, though serious infections and outbreaks have been reported from time to time. Some have suggested that P. putida functions as an exchange platform for antibiotic resistance genes (ARG), and thus represents a serious concern in the spread of ARGs to more pathogenic organisms within a hospital. Though poorly understood, the frequency of ARG exchange between P...
November 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29124862/catabolic-task-division-between-two-interchangeable-near-isogenic-subpopulations-co-existing-in-a-herbicide-degrading-bacterial-consortium-consequences-for-the-interspecies-consortium-metabolic-model
#14
Pieter Albers, Cédric Lood, Basak Özturk, Benjamin Horemans, Rob Lavigne, Vera van Noort, René De Mot, Kathleen Marchal, Aminael Sanchez-Rodriguez, Dirk Springael
Variovorax sp. WDL1 mediates hydrolysis of the herbicide linuron into 3,4-dichloroaniline (DCA) and N,O-dimethylhydroxylamine in a tripartite bacterial consortium with Comamonas testosteroni WDL7 and Hyphomicrobium sulfonivorans WDL6. Although strain WDL1 contains the dcaQTA1A2B operon for DCA oxidation, this conversion is mainly performed by WDL7. Phenotypic diversification observed in WDL1 cultures and scrutiny of the WDL1 genome suggest that WDL1 cultures consist of two dedicated subpopulations, i.e., a linuron-hydrolyzing subpopulation (Lin+DCA-) and a DCA-oxidizing subpopulation (Lin-DCA+)...
November 10, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29120256/silent-but-deadly-is200-promotes-pathogenicity-in-salmonella-typhimurium
#15
Michael J Ellis, Lindsey A Carfrae, Craig R Macnair, Ryan S Trussler, Eric D Brown, David B Haniford
Bacterial transposons were long thought of as selfish mobile genetic elements that propagate at the expense of 'host' bacterium fitness. However, limited transposition can benefit the host organism by promoting DNA rearrangements and facilitating horizontal gene transfer. Here we discuss and provide context for our recently published work which reported the surprising finding that an otherwise dormant transposon, IS200, encodes a regulatory RNA in Salmonella Typhimurium. This previous work identified a trans-acting sRNA that is encoded in the 5'UTR of IS200 transposase mRNA (tnpA)...
November 9, 2017: RNA Biology
https://www.readbyqxmd.com/read/29117562/primer-independent-dna-synthesis-by-a-family-b-dna-polymerase-from-self-replicating-mobile-genetic-elements
#16
Modesto Redrejo-Rodríguez, Carlos D Ordóñez, Mónica Berjón-Otero, Juan Moreno-González, Cristian Aparicio-Maldonado, Patrick Forterre, Margarita Salas, Mart Krupovic
Family B DNA polymerases (PolBs) play a central role during replication of viral and cellular chromosomes. Here, we report the discovery of a third major group of PolBs, which we denote primer-independent PolB (piPolB), that might be a link between the previously known protein-primed and RNA/DNA-primed PolBs. PiPolBs are encoded by highly diverse mobile genetic elements, pipolins, integrated in the genomes of diverse bacteria and also present as circular plasmids in mitochondria. Biochemical characterization showed that piPolB displays efficient DNA polymerization activity that can use undamaged and damaged templates and is endowed with proofreading and strand displacement capacities...
November 7, 2017: Cell Reports
https://www.readbyqxmd.com/read/29112896/staphylococcal-food-poisoning-caused-by-staphylococcus-argenteus-harboring-staphylococcal-enterotoxin-genes
#17
Yuki Wakabayashi, Kaoru Umeda, Shinya Yonogi, Hiromi Nakamura, Kaori Yamamoto, Yuko Kumeda, Kentaro Kawatsu
Staphylococcal food poisoning (SFP) is caused by staphylococcal enterotoxins (SEs) preformed in food materials. SE genes are encoded on mobile genetic elements and are widely found across Staphylococcus species including S. argenteus, although most SFP cases are caused by S. aureus. S. argenteus, recently discriminated from S. aureus as a novel species, are non-pigmented staphylococci phenotypically related to S. aureus. In 2014 and 2015, two independent food poisoning cases occurred in Osaka, Japan, in which non-pigmented staphylococci were predominantly isolated...
October 22, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29106666/tadb-2-0-an-updated-database-of-bacterial-type-ii-toxin-antitoxin-loci
#18
Yingzhou Xie, Yiqing Wei, Yue Shen, Xiaobin Li, Hao Zhou, Cui Tai, Zixin Deng, Hong-Yu Ou
TADB2.0 (http://bioinfo-mml.sjtu.edu.cn/TADB2/) is an updated database that provides comprehensive information about bacterial type II toxin-antitoxin (TA) loci. Compared with the previous version, the database refined and the new data schema is employed. With the aid of text mining and manual curation, it recorded 6193 type II TA loci in 870 replicons of bacteria and archaea, including 105 experimentally validated TA loci. In addition, the newly developed tool TAfinder combines the homolog searches and the operon structure detection, allowing the prediction for type II TA pairs in bacterial genome sequences...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29099338/messing-up-translation-from-the-start-how-atat-inhibits-translation-initiation-in-e-coli
#19
Laurence Van Melderen, Dukas Jurenas, Abel Garcia-Pino
Toxin---antitoxin systems (TA) are widespread in bacteria and archea. They are commonly found in chromosomes and mobile genetic elements. These systems move from different genomic locations and bacterial hosts through horizontal gene transfer, using mobile elements as vehicles. Their potential roles in bacterial physiology are still a matter of debate in the field. The mechanisms of action of different toxin families have been deciphered at the molecular level. Intriguingly, the vast majority of these toxins target protein synthesis...
November 3, 2017: RNA Biology
https://www.readbyqxmd.com/read/29097664/high-frequency-recombination-between-members-of-an-ltr-retrotransposon-family-during-transposition-bursts
#20
Diego H Sanchez, Hervé Gaubert, Hajk-Georg Drost, Nicolae Radu Zabet, Jerzy Paszkowski
Retrotransposons containing long terminal repeats (LTRs) form a substantial fraction of eukaryotic genomes. The timing of past transposition can be estimated by quantifying the accumulation of mutations in initially identical LTRs. This way, retrotransposons are divided into young, potentially mobile elements, and old that moved thousands or even millions of years ago. Both types are found within a single retrotransposon family and it is assumed that the old members will remain immobile and degenerate further...
November 3, 2017: Nature Communications
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