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Mobile genome element

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https://www.readbyqxmd.com/read/28324178/complete-genome-sequence-analysis-of-a-novel-staphylococcus-phage-stap1-and-proposal-of-a-new-species-in-the-genus-silviavirus
#1
Amal Senevirathne, Kuntal Ghosh, Eunjung Roh, Kwang-Pyo Kim
Bacteriophage StAP1 was isolated from a soil sample infecting Staphylococcus aureus and S. xylosus. Its genome was found to be 135,502 base pairs (bp) long with 30.00 mol% G+C content and 192 open reading frames. While no tRNA encoding genes were identified, 7 mobile elements were found to interrupt five StAP1 open reading frames. Comparative genomic and proteomic analysis consistently supports the establishment of a new species in the genus Silviavirus.
March 21, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28319117/comparative-genomics-of-clavibacter-michiganensis-subspecies-pathogens-of-important-agricultural-crops
#2
James T Tambong
Subspecies of Clavibacter michiganensis are important phytobacterial pathogens causing devastating diseases in several agricultural crops. The genome organizations of these pathogens are poorly understood. Here, the complete genomes of 5 subspecies (C. michiganensis subsp. michiganensis, Cmi; C. michiganensis subsp. sepedonicus, Cms; C. michiganensis subsp. nebraskensis, Cmn; C. michiganensis subsp. insidiosus, Cmi and C. michiganensis subsp. capsici, Cmc) were analyzed. This study assessed the taxonomic position of the subspecies based on 16S rRNA and genome-based DNA homology and concludes that there is ample evidence to elevate some of the subspecies to species-level...
2017: PloS One
https://www.readbyqxmd.com/read/28319081/guide-independent-dna-cleavage-by-archaeal-argonaute-from-methanocaldococcus-jannaschii
#3
Adrian Zander, Sarah Willkomm, Sapir Ofer, Marleen van Wolferen, Luisa Egert, Sabine Buchmeier, Sarah Stöckl, Philip Tinnefeld, Sabine Schneider, Andreas Klingl, Sonja-Verena Albers, Finn Werner, Dina Grohmann
Prokaryotic Argonaute proteins acquire guide strands derived from invading or mobile genetic elements, via an unknown pathway, to direct guide-dependent cleavage of foreign DNA. Here, we report that Argonaute from the archaeal organism Methanocaldococcus jannaschii (MjAgo) possesses two modes of action: the canonical guide-dependent endonuclease activity and a non-guided DNA endonuclease activity. The latter allows MjAgo to process long double-stranded DNAs, including circular plasmid DNAs and genomic DNAs...
March 20, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28315021/clinical-strains-of-streptococcus-agalactiae-carry-two-different-variants-of-pathogenicity-island-xii
#4
Eugenia Kuleshevich, Joseph Ferretti, Ilda Santos Sanches, Natesan Balasubramanian, Barbara Spellerberg, Androulla Efstratiou, Paula Kriz, Kornelia Grabovskaya, Olga Arjanova, Alevtina Savitcheva, Valentin Shevchenko, Anton Rysev, Alexander Suvorov
Streptococcus agalactiae or Group B streptococci (GBS) are a common cause of serious diseases of newborns and adults. GBS pathogenicity largely depends on genes located on the accessory genome including several pathogenicity islands (PAI). The present paper is focused on the structure and molecular epidemiological analysis of one of the GBS pathogenicity islands-the pathogenicity island PAI XII (Glaser et al. Mol Microbiol 45(6):1499-1513, 2002). This PAI was found to be composed of three different mobile genetic elements: a composite transposon (PAI-C), a genomic islet (PAI-B), and a pathogenicity island associated with gene sspB1 (PAI-A)...
March 18, 2017: Folia Microbiologica
https://www.readbyqxmd.com/read/28304213/characterization-of-the-genetic-environment-of-the-blaveb-4-gene-associated-with-a-transposable-region-in-a-proteus-mirabilis-clinical-isolate
#5
Paula Espinal, Elisenda Miró, Laia Ramoneda, Manel Flores, Alba Rivera, Pere Coll, Ferran Navarro
Proteus mirabilis is the second most common cause of urinary tract infections and is also an important cause of nosocomial infections. TEM-type and CTX-M-type extended-spectrum β-lactamases (ESBLs) are the most widely distributed in this bacterial species, but minor ESBLs such as the VEB-type have also been identified. The aim of this study was to analyze the genetic environment of the blaVEB-4 gene found in a P. mirabilis clinical isolate recovered in Spain. P. mirabilis N2231 showed resistance to penicillins, cephalosporins, and aminoglycosides, remaining susceptible to imipenem, cefoxitin, β-lactamases inhibitors, and quinolones...
March 17, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28302782/genome-sequences-of-mycobacteriophages-jane-and-sneeze-new-members-of-cluster-g
#6
Catherine M Mageeney, Cimrin Bhalla, Charles A Bowman, Bhavishya Devireddy, Adrienne P Dzurick, Lee H Graham, Marina Grossi, Margaret A Kenna, Mikala A Kowal, Drew D Nielsen, Rachel A Pallay, Kaitlyn M Ruffing, Daniel A Russell, Samantha L Sarli, Adama Shaw, Joseph W Skibbens, Joseph N Teyim, Vassie C Ware
Jane and Sneeze are newly isolated phages of Mycobacterium smegmatis mc(2)155 from Hillsborough, NJ, and Palo Verde, Costa Rica, respectively. Both are cluster G, subcluster G1 mycobacteriophages. Notable nucleotide differences exist between genomes in the right half, including the presence of mycobacteriophage mobile element 1 (MPME1) in Jane.
March 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28293680/comparative-genome-analyses-of-vibrio-anguillarum-strains-reveal-a-link-with-pathogenicity-traits
#7
Daniel Castillo, Paul D Alvise, Ruiqi Xu, Faxing Zhang, Mathias Middelboe, Lone Gram
Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity...
January 2017: MSystems
https://www.readbyqxmd.com/read/28283023/genome-analysis-following-a-national-increase-in-scarlet-fever-in-england-2014
#8
Victoria Chalker, Aleksey Jironkin, Juliana Coelho, Ali Al-Shahib, Steve Platt, Georgia Kapatai, Roger Daniel, Chenchal Dhami, Marisa Laranjeira, Timothy Chambers, Rebecca Guy, Theresa Lamagni, Timothy Harrison, Meera Chand, Alan P Johnson, Anthony Underwood
BACKGROUND: During a substantial elevation in scarlet fever (SF) notifications in 2014 a national genomic study was undertaken of Streptococcus pyogenes (Group A Streptococci, GAS) isolates from patients with SF with comparison to isolates from patients with invasive disease (iGAS) to test the hypotheses that the increase in SF was due to either the introduction of one or more new/emerging strains in the population in England or the transmission of a known genetic element through the population of GAS by horizontal gene transfer (HGT) resulting in infections with an increased likelihood of causing SF...
March 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28278261/evolutionary-and-biogeographical-implications-of-degraded-laglidadg-endonuclease-functionality-and-group-i-intron-occurrence-in-stony-corals-scleractinia-and-mushroom-corals-corallimorpharia
#9
Juan Sebastián Celis, David R Edgell, Björn Stelbrink, Daniel Wibberg, Torsten Hauffe, Jochen Blom, Jörn Kalinowski, Thomas Wilke
Group I introns and homing endonuclease genes (HEGs) are mobile genetic elements, capable of invading target sequences in intron-less genomes. LAGLIDADG HEGs are the largest family of endonucleases, playing a key role in the mobility of group I introns in a process known as 'homing'. Group I introns and HEGs are rare in metazoans, and can be mainly found inserted in the COXI gene of some sponges and cnidarians, including stony corals (Scleractinia) and mushroom corals (Corallimorpharia). Vertical and horizontal intron transfer mechanisms have been proposed as explanations for intron occurrence in cnidarians...
2017: PloS One
https://www.readbyqxmd.com/read/28270110/comparative-genomics-of-enterococcus-spp-isolated-from-bovine-feces
#10
Alicia G Beukers, Rahat Zaheer, Noriko Goji, Kingsley K Amoako, Alexandre V Chaves, Michael P Ward, Tim A McAllister
BACKGROUND: Enterococcus is ubiquitous in nature and is a commensal of both the bovine and human gastrointestinal (GI) tract. It is also associated with clinical infections in humans. Subtherapeutic administration of antibiotics to cattle selects for antibiotic resistant enterococci in the bovine GI tract. Antibiotic resistance genes (ARGs) may be present in enterococci following antibiotic use in cattle. If located on mobile genetic elements (MGEs) their dissemination between Enterococcus species and to pathogenic bacteria may be promoted, reducing the efficacy of antibiotics...
March 8, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28264559/a-family-of-single-copy-repabc-type-shuttle-vectors-stably-maintained-in-the-alpha-proteobacterium-sinorhizobium-meliloti
#11
Johannes Döhlemann, Marcel Wagner, Carina Happel, Martina Carrillo, Patrick Sobetzko, Tobias J Erb, Martin Thanbichler, Anke Becker
A considerable share of bacterial species maintains segmented genomes. Plant symbiotic α-proteobacterial rhizobia contain up to six repABC-type replicons in addition to the primary chromosome. These low or unit-copy replicons, classified as secondary chromosomes, chromids, or megaplasmids, are exclusively found in α-proteobacteria. Replication and faithful partitioning of these replicons to the daughter cells is mediated by the repABC region. The importance of α-rhizobial symbiotic nitrogen fixation for sustainable agriculture and Agrobacterium-mediated plant transformation as a tool in plant sciences has increasingly moved biological engineering of these organisms into focus...
March 20, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28263906/characterization-of-genetic-determinants-involved-in-antibiotic-resistance-in-aeromonas-spp-and-fecal-coliforms-isolated-from-different-aquatic-environments
#12
Alessandro Carnelli, Federica Mauri, Antonella Demarta
Aeromonas spp. and fecal coliforms, two abundant and cultivable bacterial populations that can be found in water ecosystems, might substantially contribute to the spread of antibiotic resistance. We investigated the presence and spread of transposons (elements that can move from one location to another in the genome), integrons (structures able to capture and incorporate gene cassettes) and resistance plasmids in strains isolated from polluted and unpolluted water. We recovered 231 Aeromonas and 250 fecal coliforms from water samplings with different degrees of pollution (hospital sewage, activated sludge of a wastewater treatment plant, river water before and after treatment and water from an alpine lake)...
March 2, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28257489/analysis-of-the-complete-genome-sequence-of-nocardia-seriolae-utf1-the-causative-agent-of-fish-nocardiosis-the-first-reference-genome-sequence-of-the-fish-pathogenic-nocardia-species
#13
Motoshige Yasuike, Issei Nishiki, Yuki Iwasaki, Yoji Nakamura, Atushi Fujiwara, Yoshiko Shimahara, Takashi Kamaishi, Terutoyo Yoshida, Satoshi Nagai, Takanori Kobayashi, Masaya Katoh
Nocardiosis caused by Nocardia seriolae is one of the major threats in the aquaculture of Seriola species (yellowtail; S. quinqueradiata, amberjack; S. dumerili and kingfish; S. lalandi) in Japan. Here, we report the complete nucleotide genome sequence of N. seriolae UTF1, isolated from a cultured yellowtail. The genome is a circular chromosome of 8,121,733 bp with a G+C content of 68.1% that encodes 7,697 predicted proteins. In the N. seriolae UTF1 predicted genes, we found orthologs of virulence factors of pathogenic mycobacteria and human clinical Nocardia isolates involved in host cell invasion, modulation of phagocyte function and survival inside the macrophages...
2017: PloS One
https://www.readbyqxmd.com/read/28251870/genomic-exaptation-enables-lasius-niger-adaptation-to-urban-environments
#14
Evgenii A Konorov, Mikhail A Nikitin, Kirill V Mikhailov, Sergey N Lysenkov, Mikhail Belenky, Peter L Chang, Sergey V Nuzhdin, Victoria A Scobeyeva
BACKGROUND: The world is rapidly urbanizing, and only a subset of species are able to succeed in stressful city environments. Efficient genome-enabled stress response appears to be a likely prerequisite for urban adaptation. Despite the important role ants play in the ecosytem, only the genomes of ~13 have been sequenced so far. Here, we present the draft genome assembly of the black garden ant Lasius niger - the most successful urban inhabitant of all ants - and we compare it with the genomes of other ant species, including the closely related Camponotus floridanus...
February 7, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28247934/anti-crispr-proteins-counterattack-of-phages-on-bacterial-defense-crispr-cas-system
#15
Kulbhushan Chaudhary, Anirudha Chattopadhyay, Dharmendra Pratap
Since the dawn of life there is a never ending strife between bacteria and phages. Both are perpetually changing their strategies to take over each other. CRISPR/Cas is the most widespread defense system used by bacteria against mobile genetic elements (MGEs) such as phages, cojugative palsmids, transoposons and pathogenicity islands. This system utilizes small guide RNA molecules to protect against phages infection and invasion by MGEs. Phages circumvent to these antiviral barriers by point mutation in PAM (protospacer-adjacent motif) sequence, genome rearrangements and by using anti-CRISPR proteins...
March 1, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28247474/conflicting-selection-alters-the-trajectory-of-molecular-evolution-in-a-tripartite-bacteria-plasmid-phage-interaction
#16
Ellie Harrison, James J P Hall, Steve Paterson, Andrew J Spiers, Michael A Brockhurst
Bacteria engage in a complex network of ecological interactions, which includes mobile genetic elements (MGEs) such as phages and plasmids. These elements play a key role in microbial communities as vectors of horizontal gene transfer but can also be important sources of selection for their bacterial hosts. In natural communities bacteria are likely to encounter multiple MGEs simultaneously and conflicting selection among MGEs could alter the bacterial evolutionary response to each MGE. Here we test the effect of interactions with multiple MGEs on bacterial molecular evolution in the tripartite interaction between the bacterium, Pseudomonas fluorescens, the lytic bacteriophage SBW25φ2 and conjugative plasmid, pQBR103, using genome sequencing of experimentally evolved bacteria...
March 1, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28245154/crispr-cas-technologies-and-applications-in-food-bacteria
#17
Emily Stout, Todd Klaenhammer, Rodolphe Barrangou
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form adaptive immune systems that occur in many bacteria and most archaea. In addition to protecting bacteria from phages and other invasive mobile genetic elements, CRISPR-Cas molecular machines can be repurposed as tool kits for applications relevant to the food industry. A primary concern of the food industry has long been the proper management of food-related bacteria, with a focus on both enhancing the outcomes of beneficial microorganisms such as starter cultures and probiotics and limiting the presence of detrimental organisms such as pathogens and spoilage microorganisms...
February 28, 2017: Annual Review of Food Science and Technology
https://www.readbyqxmd.com/read/28240206/-dna-sequences-from-mobile-genetic-elements-a-hidden-half-of-the-human-genome
#18
Julie Medina, Hervé Perron
Current data estimate that mobile genetic elements represent more than one-half of the human genome. The literature is constantly updating data following the evolution of sequencing techniques and of algorithms for genome analyses. This review aims to provide an overview of the topic showing the complexity given by the various designations and classifications found in scientific papers. A particular focus is made on retrotransposons, including Endogenous RetroViruses (ERV), to introduce a second article focusing on their activation and their involvement in physiological functions and/or pathological mechanisms associated with diseases like multiple sclerosis (MS) or amyotrophic lateral sclerosis (ALS)...
February 2017: Médecine Sciences: M/S
https://www.readbyqxmd.com/read/28238733/fragmentation-of-the-crispr-cas-type-i-b-signature-protein-cas8b
#19
Hagen Richter, Judith Rompf, Julia Wiegel, Kristina Rau, Lennart Randau
BACKGROUND: CRISPR arrays are transcribed into long precursor RNA species, which are further processed into mature CRISPR RNAs (crRNAs). Cas proteins utilize these crRNAs, which contain spacer sequences that can be derived from mobile genetic elements, to mediate immunity during a reoccurring virus infection. Type I CRISPR-Cas systems are defined by the presence of different Cascade interference complexes containing large and small subunits that play major roles during target DNA selection...
February 24, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28223389/analysis-of-serial-isolates-of-mcr-1-positive-escherichia-coli-reveals-a-highly-active-isapl1-transposon
#20
Erik Snesrud, Ana C Ong, Brendan Corey, Yoon I Kwak, Robert Clifford, Todd Gleeson, Shannon Wood, Timothy J Whitman, Emil P Lesho, Mary Hinkle, Patrick Mc Gann
The emergence of the transferable colistin resistance gene mcr-1 is of global concern. The insertion sequence (IS) Apl1 is a key component in the mobilization of this gene, but its role remains poorly understood.Six Escherichia coli were cultured from the same patient over one month in Germany and the USA after a brief hospitalization in Bahrain for an unconnected illness. Four carried mcr-1 by real-time PCR, but two were negative. Two additional mcr-1-negative E. coli were collected during follow-up surveillance nine months later...
February 21, 2017: Antimicrobial Agents and Chemotherapy
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