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Mobile genetic element

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https://www.readbyqxmd.com/read/28334919/antibiotics-trigger-initiation-of-sccmec-transfer-by-inducing-sos-responses
#1
Pilong Liu, Zhaowei Wu, Huping Xue, Xin Zhao
The rise of antimicrobial resistance limits therapeutic options for infections by methicillin-resistant staphylococci. The staphylococcal cassette chromosome mec (SCCmec) is a mobile genetic element as the only carrier of the methicillin-resistance determinants, the mecA or mecC gene. The use of antibiotics increases the spread of antibiotic resistance, but the mechanism by which antibiotics promote horizontal dissemination of SCCmec is largely unknown. In this study, we demonstrate that many antibiotics, including β-lactams, can induce the expression of ccrC1 and SCCmec excision from the bacterial chromosome...
March 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334706/repetitive-dna-a-versatile-tool-for-karyotyping-in-festuca-pratensis-huds
#2
Anna Křivánková, David Kopecký, Štěpán Stočes, Jaroslav Doležel, Eva Hřibová
FISH is a useful method to identify individual chromosomes in a karyotype and to discover their structural changes accompanying genome evolution and speciation. DNA probes for FISH should be chromosome specific and/or exhibit specific patterns of distribution along each chromosome. Such probes are not available in many plants including meadow fescue (Festuca pratensis Huds.), an important forage grass species. In the present study, various DNA repeats identified in Illumina shotgun sequences specific to chromosome 4F of F...
March 24, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28331090/hili-inhibits-hiv-replication-in-activated-t-cells
#3
B Matija Peterlin, Pingyang Liu, Xiaoyun Wang, Daniele Cary, Wei Shao, Marie Leoz, Tian Hong, Tao Pan, Koh Fujinaga
Piwil proteins restrict the replication of mobile genetic elements in the germline. They are also expressed in many transformed cell lines. In this report, we discovered that the human piwil 2 (hili) can also inhibit HIV replication, especially in activated CD4+ T cells that are the preferred target cells for this virus in the infected host. Although resting cells did not express hili, it was rapidly induced following T cell activation. In these cells and transformed cell lines, depletion of hili increased levels of viral proteins and new viral particles...
March 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28327913/the-use-of-oxford-nanopore-native-barcoding-for-complete-genome-assembly
#4
Sion C Bayliss, Vicky L Hunt, Maho Yokoyama, Harry A Thorpe, Edward J Feil
Background: The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short-read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short-read data...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28319081/guide-independent-dna-cleavage-by-archaeal-argonaute-from-methanocaldococcus-jannaschii
#5
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
#6
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
#7
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/28299457/current-trends-of-human-infections-and-antibiotic-resistance-of-the-genus-shewanella
#8
REVIEW
K Yousfi, S Bekal, V Usongo, A Touati
Shewanella spp. are commonly known as environmental bacteria and are most frequently isolated from aquatic areas. Currently, diseases syndromes and multidrug resistance have increasingly been reported in the genus Shewanella. Some species are associated with various infections, such as skin and soft tissue infections, as well as bacteremia. Generally, these bacteria are opportunistic and mostly affect people with an impaired immune system. This genus is also a probable vehicle and progenitor of antibiotic resistance genes...
March 15, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28293680/comparative-genome-analyses-of-vibrio-anguillarum-strains-reveal-a-link-with-pathogenicity-traits
#9
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/28284599/the-oral-microbiota-of-domestic-cats-harbors-a-wide-variety-of-staphylococcus-species-with-zoonotic-potential
#10
Ciro César Rossi, Ingrid da Silva Dias, Igor Mansur Muniz, Walter Lilenbaum, Marcia Giambiagi-deMarval
This study aimed to characterize the species, antimicrobial resistance and dispersion of CRISPR systems in staphylococci isolated from the oropharynx of domestic cats in Brazil. Staphylococcus strains (n=75) were identified by MALDI-TOF and sequencing of rpoB and tuf genes. Antimicrobial susceptibility was assessed by disk diffusion method and PCR to investigate the presence of antimicrobial-resistance genes usually present in mobile genetic elements (plasmids), in addition to plasmid extraction. CRISPR - genetic arrangements that give the bacteria the ability to resist the entry of exogenous DNA - were investigated by the presence of the essential protein Cas1 gene...
March 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28283023/genome-analysis-following-a-national-increase-in-scarlet-fever-in-england-2014
#11
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/28282376/the-transjugation-machinery-of-thermus-thermophilus-identification-of-tdta-an-atpase-involved-in-dna-donation
#12
Alba Blesa, Ignacio Baquedano, Nieves G Quintáns, Carlos P Mata, José R Castón, José Berenguer
In addition to natural competence, some Thermus thermophilus strains show a high rate of DNA transfer via direct cell-to-cell contact. The process is bidirectional and follows a two-step model where the donor cell actively pushes out DNA and the recipient cell employs the natural competence system to take up the DNA, in a hybrid transformation-dependent conjugation process (transjugation). While the DNA uptake machinery is well known as in other bacterial species that undergo transformation, the pushing step of transjugation remains to be characterized...
March 2017: PLoS Genetics
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
#13
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
#14
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/28264992/crispr-cas-and-contact-dependent-secretion-systems-present-on-excisable-pathogenicity-islands-with-conserved-recombination-modules
#15
Megan R Carpenter, Sai S Kalburge, Joseph D Borowski, Molly C Peters, Rita R Colwell, E Fidelma Boyd
Pathogenicity islands (PAIs) are mobile integrated genetic elements that contain a diverse range of virulence factors. PAIs integrate into the host chromosome at a tRNA locus that contains their specific bacterial attachment site, attB, via integrase mediated site-specific recombination generating attL and attR sites. We identified conserved recombination modules (integrases and att sites) previously described in choleragenic V. cholerae PAIs but with novel cargo genes. Clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins) and a type VI secretion system (T6SS) gene cluster were identified at the Vibrio Pathogenicity Island-1 (VPI-1) insertion site in nineteen V...
March 6, 2017: Journal of Bacteriology
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
#16
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/28257056/interaction-of-type-iv-toxin-antitoxin-systems-in-cryptic-prophages-of-escherichia-coli-k-12
#17
Zhongling Wen, Pengxia Wang, Chenglong Sun, Yunxue Guo, Xiaoxue Wang
Toxin/antitoxin (TA) systems are widespread in prokaryotic chromosomes and in mobile genetic elements including plasmids and prophages. The first characterized Type IV TA system CbtA/CbeA was found in cryptic prophage CP4-44 in Escherichia coli K-12. Two homologous TA loci of CbtA/CbeA also reside in cryptic prophages of E. coli K-12, YkfI/YafW in CP4-6 and YpjF/YfjZ in CP4-57. In this study, we demonstrated that YkfI and YpjF inhibited cell growth and led to the formation of "lemon-shaped" cells. Prolonged overproduction of YkfI led to the formation of "gourd-shaped" cells and immediate cell lysis...
March 1, 2017: Toxins
https://www.readbyqxmd.com/read/28247934/anti-crispr-proteins-counterattack-of-phages-on-bacterial-defense-crispr-cas-system
#18
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
#19
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
#20
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
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