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Mobile genome element

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https://www.readbyqxmd.com/read/29346643/genetic-characterization-of-a-vang-type-vancomycin-resistant-enterococcus-faecium-clinical-isolate
#1
Mohamed Sassi, François Guérin, Léonie Lesec, Christophe Isnard, Marguerite Fines-Guyon, Vincent Cattoir, Jean-Christophe Giard
Objectives: To characterize, phenotypically and genotypically, the first Enterococcus faecium clinical isolate harbouring a vanG operon. Methods: The antibiotic resistance profile of E. faecium 16-346 was determined and its whole genome sequenced using PacBio technology. Attempts to transfer vancomycin resistance by filter mating were performed and the inducibility of expression of the vanG operon was studied by reverse-transcription quantitative PCR (RT-qPCR) in the presence or absence of subinhibitory concentrations of vancomycin...
January 16, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29346586/plasflow-predicting-plasmid-sequences-in-metagenomic-data-using-genome-signatures
#2
Pawel S Krawczyk, Leszek Lipinski, Andrzej Dziembowski
Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29342280/epigenetic-differentiation-of-natural-populations-of-lilium-bosniacum-associated-with-contrasting-habitat-conditions
#3
V Zoldoš, I Biruš, E Muratovic, Z Šatovic, A Vojta, O Robin, F Pustahija, F Bogunic, V Vicic Bockor, S Siljak-Yakovlev
Epigenetic variation in natural populations with contrasting habitats might be an important element, in addition to the genetic variation, in plant adaptation to environmental stress. Here, we assessed genetic, epigenetic and cytogenetic structure of the three Lilium bosniacum populations growing on distinct habitats. One population was growing under habitual ecological conditions for this species and the other two were growing under stress associated with high altitude and serpentine soil. Amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) analyses revealed that the three populations did not differentiate genetically, but were clearly separated in the three distinct clusters according to DNA methylation profiles...
January 12, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29339760/biochemical-and-genetic-characterization-of-a-novel-metallo-%C3%AE-lactamase-from-marine-bacterium-erythrobacter-litoralis-htcc-2594
#4
Xia-Wei Jiang, Hong Cheng, Ying-Yi Huo, Lin Xu, Yue-Hong Wu, Wen-Hong Liu, Fang-Fang Tao, Xin-Jie Cui, Bei-Wen Zheng
Metallo-β-lactamases (MBLs) are a group of enzymes that can inactivate most commonly used β-lactam-based antibiotics. Among MBLs, New Delhi metallo-β-lactamase-1 (NDM-1) constitutes an urgent threat to public health as evidenced by its success in rapidly disseminating worldwide since its first discovery. Here we report the biochemical and genetic characteristics of a novel MBL, ElBla2, from the marine bacterium Erythrobacter litoralis HTCC 2594. This enzyme has a higher amino acid sequence similarity to NDM-1 (56%) than any previously reported MBL...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29327410/genomic-insights-into-the-acidobacteria-reveal-strategies-for-their-success-in-terrestrial-environments
#5
Stephanie A Eichorst, Daniela Trojan, Simon Roux, Craig Herbold, Thomas Rattei, Dagmar Woebken
Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed the largest (to date) comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8, and 23 (n=24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. In contrast to earlier studies, our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low- and high-affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients...
January 12, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29288557/alu-element-insertion-in-pklr-gene-as-a-novel-cause-of-pyruvate-kinase-deficiency-in-middle-eastern-patients
#6
Harry Lesmana, Lisa Dyer, Xia Li, James Denton, Jenna Griffiths, Satheesh Chonat, Katie G Seu, Matthew M Heeney, Kejian Zhang, Robert J Hopkin, Theodosia A Kalfa
Pyruvate kinase deficiency (PKD) is the most frequent red blood cell enzyme abnormality of the glycolytic pathway and the most common cause of hereditary nonspherocytic hemolytic anemia. Over 250 PKLR-gene mutations have been described, including missense/nonsense, splicing and regulatory mutations, small insertions, small and gross deletions, causing PKD and hemolytic anemia of variable severity. Alu retrotransposons are the most abundant mobile DNA sequences in the human genome, contributing to almost 11% of its mass...
December 30, 2017: Human Mutation
https://www.readbyqxmd.com/read/29287670/investigation-of-clostridium-botulinum-group-iii-s-mobilome-content
#7
Cédric Woudstra, Caroline Le Maréchal, Rozenn Souillard, Fabrizio Anniballi, Bruna Auricchio, Luca Bano, Marie-Hélène Bayon-Auboyer, Miriam Koene, Isabelle Mermoud, Roseane B Brito, Francisco C F Lobato, Rodrigo O S Silva, Martin B Dorner, Patrick Fach
Clostridium botulinum group III is mainly responsible for botulism in animals. It could lead to high animal mortality rates and, therefore, represents a major environmental and economic concern. Strains of this group harbor the botulinum toxin locus on an unstable bacteriophage. Since the release of the first complete C. botulinum group III genome sequence (strain BKT015925), strains have been found to contain others mobile elements encoding for toxin components. In this study, seven assays targeting toxin genes present on the genetic mobile elements of C...
December 26, 2017: Anaerobe
https://www.readbyqxmd.com/read/29281823/rna-independent-dna-cleavage-activities-of-cas9-and-cas12a
#8
Ramya Sundaresan, Hari Priya Parameshwaran, S D Yogesha, Mark Walter Keilbarth, Rakhi Rajan
CRISPR-Cas systems provide bacteria and archaea with sequence-specific protection against invading mobile genetic elements. In the presence of divalent metal ions, Cas9 and Cas12a (formerly Cpf1) proteins target and cleave DNA that is complementary to a cognate guide RNA. The recognition of a protospacer adjacent motif (PAM) sequence in the target DNA by Cas9 and Cas12a is essential for cleavage. This RNA-guided DNA targeting is widely used for gene-editing methods. Here, we show that Francisella tularensis novicida (Fno) Cas12a, FnoCas9, and Streptococcus pyogenes Cas9 (SpyCas9) cleave DNA without a guide RNA in the presence of Mn2+ ions...
December 26, 2017: Cell Reports
https://www.readbyqxmd.com/read/29277877/comparative-genomics-in-drosophila
#9
Martin Oti, Attilio Pane, Michael Sammeth
Since the pioneering studies of Thomas Hunt Morgan and coworkers at the dawn of the twentieth century, Drosophila melanogaster and its sister species have tremendously contributed to unveil the rules underlying animal genetics, development, behavior, evolution, and human disease. Recent advances in DNA sequencing technologies launched Drosophila into the post-genomic era and paved the way for unprecedented comparative genomics investigations. The complete sequencing and systematic comparison of the genomes from 12 Drosophila species represents a milestone achievement in modern biology, which allowed a plethora of different studies ranging from the annotation of known and novel genomic features to the evolution of chromosomes and, ultimately, of entire genomes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29277867/a-practical-guide-for-comparative-genomics-of-mobile-genetic-elements-in-prokaryotic-genomes
#10
Danillo Oliveira Alvarenga, Leandro M Moreira, Mick Chandler, Alessandro M Varani
Mobile genetic elements (MGEs) are an important feature of prokaryote genomes but are seldom well annotated and, consequently, are often underestimated. MGEs include transposons (Tn), insertion sequences (ISs), prophages, genomic islands (GEIs), integrons, and integrative and conjugative elements (ICEs). They are intimately involved in genome evolution and promote phenomena such as genomic expansion and rearrangement, emergence of virulence and pathogenicity, and symbiosis. In spite of the annotation bottleneck, there are so far at least 75 different programs and databases dedicated to prokaryotic MGE analysis and annotation, and this number is rapidly growing...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29277529/comparative-genomics-of-the-rmtb-carrying-inci1-st136-plasmids-in-avian-escherichia-coli-isolates-from-chickens-in-china
#11
Li Yuan, Jian-Hua Liu, Xiang-Dang Du, Zhi-Yong Zong, Min Chen, Gong-Zheng Hu, Yu-Shan Pan
Eight rmtB-carrying avian Escherichia coli strains from a farm in China were characterized in our previous study, but little is known about the backbones and entire multiresistance regions (MRRs) of these plasmids. Here, three rmtB-carrying IncI1 ST136 plasmids were analyzed by whole-plasmid sequencing and compared. These plasmids were composed of an 83,470-bp IncI1 backbone carrying genes responsible for plasmid replication, transfer, maintenance, and stability functions, and a 17,330-bp MRR for pEC006 and pEC007, and a 34,626-bp MRR for pEC008...
December 22, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29276973/molecular-and-functional-characterization-of-tumor-induced-factor-tif-hamster-homolog-of-cxcl3-gro%C3%AE-displays-tumor-suppressive-activity
#12
Lili Jin, Zhou-Fang Li, Da-Kui Wang, Meina Sun, Wei Qi, Qiang Ma, Li Zhang, Chun Chu, Elaine Y M Chan, Susanna S T Lee, Helen Wise, Ka-Fai To, Ying Shi, Naiming Zhou, Wing-Tai Cheung
Previously our lab has created a mouse ovarian xenograft model of copy number variation (CNV)-mediated G protein-coupled receptor (GPCR) MAS-driven tumorigenesis, and RNA profiling identified a putative chemokine tumor-induced factor (Tif). Sequence analysis and chemotactic study suggested that Tif was likely to be a hamster homolog of human GROγ (CXCL3) [IJC 125 (2009): 1316-1327]. In the present study, we report the molecular and functional characterization of the Tif gene. Genomic study of CHO-K1 cells indicated that Tif gene consisted of 4 exons, characterized with an antisense B1 element which is embedded in the fourth exon...
December 22, 2017: Cytokine
https://www.readbyqxmd.com/read/29250047/the-different-faces-of-rolling-circle-replication-and-its-multifunctional-initiator-proteins
#13
REVIEW
Paweł Wawrzyniak, Grażyna Płucienniczak, Dariusz Bartosik
Horizontal gene transfer (HGT) contributes greatly to the plasticity and evolution of prokaryotic and eukaryotic genomes. The main carriers of foreign DNA in HGT are mobile genetic elements (MGEs) that have extremely diverse genetic structures and properties. Various strategies are used for the maintenance and spread of MGEs, including (i) vegetative replication, (ii) transposition (and other types of recombination), and (iii) conjugal transfer. In many MGEs, all of these processes are dependent on rolling-circle replication (RCR)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29247056/genome-sequencing-links-persistent-outbreak-of-legionellosis-in-sydney-to-an-emerging-clone-of-legionella-pneumophila-st211
#14
Verlaine J Timms, Rebecca Rockett, Nathan L Bachmann, Elena Martinez, Qinning Wang, Sharon C-A Chen, Neisha Jeoffreys, Peter J Howard, Anna Smith, Sheena Adamson, Robin Gilmour, Vicky Sheppeard, Vitali Sintchenko
The city of Sydney, Australia, experienced a persistent outbreak of Legionella pneumophila serogroup 1 (Lp1) pneumonia in 2016. To elucidate the source and guide public health actions the genomes of clinical and environmental Lp1 isolates recovered over 7 weeks were examined. A total of 48 isolates from human cases and cooling towers were sequenced and compared using SNP-based, core-genome MLST and pangenome approaches. All three methods confirmed phylogenetic relatedness between isolates associated with outbreaks in the Central Business District (CBD) in March and May and Suburb 1...
December 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29239145/line-1-retrotransposons-in-healthy-and-diseased-human-brain
#15
REVIEW
Nicole A Suarez, Angela Macia, Alysson R Muotri
Long interspersed element-1 (LINE-1 or L1) is a transposable element with the ability to self-mobilize throughout the human genome. The L1 elements found in the human brain is hypothesized to date back 56 million years ago and has survived evolution, currently accounting for 17% of the human genome. L1 retrotransposition has been theorized to contribute to somatic mosaicism. This review focuses on the presence of L1 in the healthy and diseased human brain, such as in autism spectrum disorders (ASD). Throughout this exploration, we will discuss the impact L1 has on neurological disorders that can occur throughout the human lifetime...
December 14, 2017: Developmental Neurobiology
https://www.readbyqxmd.com/read/29235574/ten-principles-of-heterochromatin-formation-and-function
#16
REVIEW
Robin C Allshire, Hiten D Madhani
Heterochromatin is a key architectural feature of eukaryotic chromosomes, which endows particular genomic domains with specific functional properties. The capacity of heterochromatin to restrain the activity of mobile elements, isolate DNA repair in repetitive regions and ensure accurate chromosome segregation is crucial for maintaining genomic stability. Nucleosomes at heterochromatin regions display histone post-translational modifications that contribute to developmental regulation by restricting lineage-specific gene expression...
December 13, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29229636/topical-antibiotic-use-co-selects-for-the-carriage-of-mobile-genetic-elements-conferring-resistance-to-unrelated-antimicrobials-in-staphylococcus-aureus
#17
Glen P Carter, Mark B Schultz, Sarah L Baines, Anders Goncalves da Silva, Helen Heffernan, Audrey Tiong, Peter H Pham, Ian R Monk, Timothy P Stinear, Benjamin P Howden, Deborah A Williamson
Topical antibiotics such as mupirocin and fusidic acid are commonly used in the prevention and treatment of skin infections, particularly those caused by staphylococci. However, widespread use of these agents is associated with increased resistance to these agents, potentially limiting their efficacy. Of particular concern is the observation that resistance to topical antibiotics is often associated with multidrug resistance, suggesting that topical antibiotics may play a role in the emergence of multidrug-resistant (MDR) strains...
December 11, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29228286/cut-and-paste-transposons-in-fungi-with-diverse-lifestyles
#18
Anna Muszewska, Kamil Steczkiewicz, Marta Stepniewska-Dziubinska, Krzysztof Ginalski
Transposons (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighbourhoods and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a "cut and paste" fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches...
December 8, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29227468/metagenomic-binning-and-association-of-plasmids-with-bacterial-host-genomes-using-dna-methylation
#19
John Beaulaurier, Shijia Zhu, Gintaras Deikus, Ilaria Mogno, Xue-Song Zhang, Austin Davis-Richardson, Ronald Canepa, Eric W Triplett, Jeremiah J Faith, Robert Sebra, Eric E Schadt, Gang Fang
Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing...
December 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/29225705/using-bioinformatic-and-phylogenetic-approaches-to-classify-transposable-elements-and-understand-their-complex-evolutionary-histories
#20
REVIEW
Irina R Arkhipova
In recent years, much attention has been paid to comparative genomic studies of transposable elements (TEs) and the ensuing problems of their identification, classification, and annotation. Different approaches and diverse automated pipelines are being used to catalogue and categorize mobile genetic elements in the ever-increasing number of prokaryotic and eukaryotic genomes, with little or no connectivity between different domains of life. Here, an overview of the current picture of TE classification and evolutionary relationships is presented, updating the diversity of TE types uncovered in sequenced genomes...
2017: Mobile DNA
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