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Horizontal DNA transfer

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https://www.readbyqxmd.com/read/27922269/genomic-study-of-the-type-ivc-secretion-system-in-clostridium-difficile-understanding-c-difficile-evolution-via-horizontal-gene-transfer
#1
Wen Zhang, Ying Cheng, Pengcheng Du, Yuanyuan Zhang, Hongbing Jia, Xianping Li, Jing Wang, Na Han, Yujun Qiang, Chen Chen, Jinxing Lu
Clostridium difficile, the etiological agent of Clostridium difficile infection (CDI), is a gram-positive, spore-forming bacillus that is responsible for ∼20% of antibiotic-related cases of diarrhea and nearly all cases of pseudomembranous colitis. Previous data have shown that a substantial proportion (11%) of the C. difficile genome consists of mobile genetic elements, including seven conjugative transposons. However, the mechanism underlying the formation of a mosaic genome in C. difficile is unknown. The type-IV secretion system (T4SS) is the only secretion system known to transfer DNA segments among bacteria...
August 30, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/27919802/integrative-view-of-2-oxoglutarate-fe-ii-dependent-oxygenase-diversity-and-functions-in-bacteria
#2
Baolei Jia, Xiaomeng Jia, Kyung Hyun Kim, Che Ok Jeon
BACKGROUND: The 2-oxoglutarate/Fe(II)-dependent oxygenase (2OG oxygenase) superfamily is extremely diverse and includes enzymes responsible for protein modification, DNA and mRNA repair, and synthesis of secondary metabolites. METHODS: To investigate the evolutionary relationship and make functional inferences within this remarkably diverse superfamily in bacteria, we used a protein sequence similarity network and other bioinformatics tools to analyze the bacterial proteins in the superfamily...
December 2, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27909941/degradation-and-half-life-of-dna-present-in-biomass-from-a-genetically-modified-organism-during-land-application
#3
Mathew C Halter, James A Zahn
White biotechnology has made a positive impact on the chemical industry by providing safer, more efficient chemical manufacturing processes that have reduced the use of toxic chemicals, harsh reaction conditions, and expensive metal catalysts, which has improved alignment with the principles of Green Chemistry. The genetically-modified (GM) biocatalysts that are utilized in these processes are typically separated from high-value products and then recycled, or eliminated. Elimination routes include disposal in sanitary landfills, incineration, use as a fuel, animal feed, or reuse as an agricultural soil amendment or other value-added products...
December 1, 2016: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/27908230/dna-import-into-mitochondria
#4
REVIEW
Yu M Konstantinov, A Dietrich, F Weber-Lotfi, N Ibrahim, E S Klimenko, V I Tarasenko, T A Bolotova, M V Koulintchenko
In recent decades, it has become evident that the condition for normal functioning of mitochondria in higher eukaryotes is the presence of membrane transport systems of macromolecules (proteins and nucleic acids). Natural competence of the mitochondria in plants, animals, and yeasts to actively uptake DNA may be directly related to horizontal gene transfer into these organelles occurring at much higher rate compared to the nuclear and chloroplast genomes. However, in contrast with import of proteins and tRNAs, little is known about the biological role and molecular mechanism underlying import of DNA into eukaryotic mitochondria...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27902367/staphylococcal-cassette-chromosome-mec-typing-and-meca-sequencing-in-methicillin-resistant-staphylococci-from-algeria-a-highly-diversified-element-with-new-mutations-in-meca
#5
Ferhat Djoudi, Celestino Bonura, Abdelaziz Touati, Aurora Aléo, Said Benallaoua, Caterina Mammina
Genetic mechanisms of methicillin resistance are still relevant in staphylococci. The aims of this study are to assess the possible exchanges of staphylococcal cassette chromosome mec (SCCmec) among isolates of methicillin-resistant staphylococci (MRS) and to check for known or new mutations in mecA DNA. A total of 35 MRS non-repetitive isolates were recovered, including 20 Staphylococcushaemolyticus, 7 Staphylococcusaureus, 4 Staphylococcussciuri, 2 Staphylococcussaprophyticus and 1 isolate each of Staphylococcusxylosus and Staphylococcuslentus...
November 2016: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/27899587/temporal-self-regulation-of-transposition-through-host-independent-transposase-rodlet-formation
#6
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/27895624/visualizing-evolutionary-relationships-of-multidomain-proteins-an-example-from-receiver-rec-domains-of-sensor-histidine-kinases-in-the-candidatus-maribeggiatoa-str-orange-guaymas-draft-genome
#7
Barbara J MacGregor
For multidomain proteins, evolutionary changes may occur at the domain as well as the whole-protein level. An example is presented here, with suggestions for how such complicated relationships might be visualized. Earlier analysis of the Candidatus Maribeggiatoa str. Orange Guaymas (BOGUAY; Gammaproteobacteria) single-filament draft genome found evidence of gene exchange with the phylogenetically distant Cyanobacteria, particularly for sensory and signal transduction proteins. Because these are modular proteins, known to undergo frequent duplication, domain swapping, and horizontal gene transfer, a single domain was chosen for analysis...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27859237/the-tetrapyrrole-synthesis-pathway-as-a-model-of-horizontal-gene-transfer-in-euglenoids
#8
Bryan Lakey, Richard Triemer
The history of euglenoids may have begun as early as ~2 bya. These early phagotrophs ate cyanobacteria, archaea and eubacteria, and the subsequent appearance of red algae and chromalveolates provided euglenoids with additional food sources. Following the appearance of green algae, euglenoids acquired a chloroplast via a secondary endosymbiotic event with a green algal ancestor. This endosymbiosis also involved a massive transfer of nuclear-encoded genes from the symbiont nucleus to the host. Expecting these genes to have a green algal origin, this research has shown, through the use of DNA-sequences and the analysis of phylogenetic relationships, that many housekeeping genes have a red algal/chromalveolate ancestry...
November 12, 2016: Journal of Phycology
https://www.readbyqxmd.com/read/27855160/transcription-factors-encoded-on-core-and-accessory-chromosomes-of-fusarium-oxysporum-induce-expression-of-effector-genes
#9
H Charlotte van der Does, Like Fokkens, Ally Yang, Sarah M Schmidt, Léon Langereis, Joanna M Lukasiewicz, Timothy R Hughes, Martijn Rep
Proteins secreted by pathogens during host colonization largely determine the outcome of pathogen-host interactions and are commonly called 'effectors'. In fungal plant pathogens, coordinated transcriptional up-regulation of effector genes is a key feature of pathogenesis and effectors are often encoded in genomic regions with distinct repeat content, histone code and rate of evolution. In the tomato pathogen Fusarium oxysporum f. sp. lycopersici (Fol), effector genes reside on one of four accessory chromosomes, known as the 'pathogenicity' chromosome, which can be exchanged between strains through horizontal transfer...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27852226/genomic-differentiation-among-wild-cyanophages-despite-widespread-horizontal-gene-transfer
#10
Ann C Gregory, Sergei A Solonenko, J Cesar Ignacio-Espinoza, Kurt LaButti, Alex Copeland, Sebastian Sudek, Ashley Maitland, Lauren Chittick, Filipa Dos Santos, Joshua S Weitz, Alexandra Z Worden, Tanja Woyke, Matthew B Sullivan
BACKGROUND: Genetic recombination is a driving force in genome evolution. Among viruses it has a dual role. For genomes with higher fitness, it maintains genome integrity in the face of high mutation rates. Conversely, for genomes with lower fitness, it provides immediate access to sequence space that cannot be reached by mutation alone. Understanding how recombination impacts the cohesion and dissolution of individual whole genomes within viral sequence space is poorly understood across double-stranded DNA bacteriophages (a...
November 16, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27849579/plant-nodulation-inducers-enhance-horizontal-gene-transfer-of-azorhizobium-caulinodans-symbiosis-island
#11
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 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27833021/natural-escherichia-coli-strains-undergo-cell-to-cell-plasmid-transformation
#12
Akiko Matsumoto, Ayuka Sekoguchi, Junko Imai, Kumiko Kondo, Yuka Shibata, Sumio Maeda
Horizontal gene transfer is a strong tool that allows bacteria to adapt to various environments. Although three conventional mechanisms of horizontal gene transfer (transformation, transduction, and conjugation) are well known, new variations of these mechanisms have also been observed. We recently reported that DNase-sensitive cell-to-cell transfer of nonconjugative plasmids occurs between laboratory strains of Escherichia coli in co-culture. We termed this phenomenon "cell-to-cell transformation." In this report, we found that several combinations of Escherichia coli collection of reference (ECOR) strains, which were co-cultured in liquid media, resulted in DNase-sensitive cell-to-cell transfer of antibiotic resistance genes...
December 2, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27825443/natural-competence-for-transformation
#13
Melanie Blokesch
While most molecular biologists are familiar with the artificial transformation of bacteria in the context of laboratory cloning experiments, natural competence for transformation refers to a specific physiological state in which prokaryotes are able to take up genetic material from their surroundings. Occasionally, such absorbed DNA is recombined into the organism's own genome, resulting in natural transformation (Figure 1). As a consequence, natural competence for transformation is considered a primary mode of horizontal gene transfer (HGT) in prokaryotes, together with conjugation (direct cell to cell transfer of DNA via a specialized conjugal pilus) and phage transduction (DNA transfer mediated by viruses)...
November 7, 2016: Current Biology: CB
https://www.readbyqxmd.com/read/27812423/proliferation-of-group-ii-introns-in-the-chloroplast-genome-of-the-green-alga-oedocladium-carolinianum-chlorophyceae
#14
Jean-Simon Brouard, Monique Turmel, Christian Otis, Claude Lemieux
BACKGROUND: The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales...
2016: PeerJ
https://www.readbyqxmd.com/read/27811049/phage-mediated-horizontal-gene-transfer-of-both-prophage-and-heterologous-dna-by-%C3%AF-bb-1-a-bacteriophage-of-borrelia-burgdorferi
#15
Christian H Eggers, Carlie M Gray, Alexander M Preisig, Danielle M Glenn, Jessica Pereira, Ryan W Ayers, Mohammad Alshahrani, Christopher Acabbo, Maria R Becker, Kimberly N Bruenn, Timothy Cheung, Taylor M Jendras, Aron B Shepley, John T Moeller
Horizontal gene transfer (HGT) in Borrelia burgdorferi, the Lyme disease agent, is likely mediated by bacteriophage. Studies of the B. burgdorferi phage, ϕBB-1, and its role in HGT have been hindered by the lack of an assay for readily characterizing phage-mediated DNA movement (transduction). Here we describe an in vitro assay in which a clone of B. burgdorferi strain CA-11.2A encoding kanamycin resistance on a ϕBB-1 prophage is co-cultured with different clones encoding gentamicin resistance on a shuttle vector; transduction is monitored by enumerating colonies selected in the presence of both kanamycin and gentamicin...
November 2, 2016: Pathogens and Disease
https://www.readbyqxmd.com/read/27791096/kinetics-of-dna-uptake-during-transformation-provide-evidence-for-a-translocation-ratchet-mechanism
#16
Christof Hepp, Berenike Maier
Horizontal gene transfer can speed up adaptive evolution and support chromosomal DNA repair. A particularly widespread mechanism of gene transfer is transformation. The initial step to transformation, namely the uptake of DNA from the environment, is supported by the type IV pilus system in most species. However, the molecular mechanism of DNA uptake remains elusive. Here, we used single-molecule techniques for characterizing the force-dependent velocity of DNA uptake by Neisseria gonorrhoeae We found that the DNA uptake velocity depends on the concentration of the periplasmic DNA-binding protein ComE, indicating that ComE is directly involved in the uptake process...
November 1, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27776538/clusterflock-a-flocking-algorithm-for-isolating-congruent-phylogenomic-datasets
#17
Apurva Narechania, Richard Baker, Rob DeSalle, Barun Mathema, Sergios-Orestis Kolokotronis, Barry Kreiswirth, Paul J Planet
BACKGROUND: Collective animal behavior, such as the flocking of birds or the shoaling of fish, has inspired a class of algorithms designed to optimize distance-based clusters in various applications, including document analysis and DNA microarrays. In a flocking model, individual agents respond only to their immediate environment and move according to a few simple rules. After several iterations the agents self-organize, and clusters emerge without the need for partitional seeds. In addition to its unsupervised nature, flocking offers several computational advantages, including the potential to reduce the number of required comparisons...
October 24, 2016: GigaScience
https://www.readbyqxmd.com/read/27765015/recent-horizontal-transfer-functional-adaptation-and-dissemination-of-a-bacterial-group-ii-intron
#18
Félix LaRoche-Johnston, Caroline Monat, Benoit Cousineau
BACKGROUND: Group II introns are catalytically active RNA and mobile retroelements present in certain eukaryotic organelles, bacteria and archaea. These ribozymes self-splice from the pre-mRNA of interrupted genes and reinsert within target DNA sequences by retrohoming and retrotransposition. Evolutionary hypotheses place these retromobile elements at the origin of over half the human genome. Nevertheless, the evolution and dissemination of group II introns was found to be quite difficult to infer...
October 20, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27751837/functional-transferred-dna-within-extracellular-vesicles
#19
Jin Cai, Gengze Wu, Pedro A Jose, Chunyu Zeng
Extracellular vesicles (EVs) are small membrane vesicles including exosomes and shedding vesicles that mediated a cell-to-cell communication. EVs are released from almost all cell types under both physiological and pathological conditions and incorporate nuclear and cytoplasmic molecules for intercellular delivery. Besides protein, mRNA, and microRNA of these molecules, as recent studies show, specific DNA are prominently packaged into EVs. It appears likely that some of exosomes or shedding vesicles, bearing nuclear molecules are released upon bubble-like blebs...
October 14, 2016: Experimental Cell Research
https://www.readbyqxmd.com/read/27736643/cgas-mediated-innate-immunity-spreads-intercellularly-through-hiv-1-env-induced-membrane-fusion-sites
#20
Shuting Xu, Aurélie Ducroux, Aparna Ponnurangam, Gabrielle Vieyres, Sergej Franz, Mathias Müsken, Thomas Zillinger, Angelina Malassa, Ellen Ewald, Veit Hornung, Winfried Barchet, Susanne Häussler, Thomas Pietschmann, Christine Goffinet
Upon sensing cytoplasmic retroviral DNA in infected cells, cyclic GMP-AMP (cGAMP) synthase (cGAS) produces the cyclic dinucleotide cGAMP, which activates STING to trigger a type I interferon (IFN) response. We find that membrane fusion-inducing contact between donor cells expressing the HIV envelope (Env) and primary macrophages endogenously expressing the HIV receptor CD4 and coreceptor enable intercellular transfer of cGAMP. This cGAMP exchange results in STING-dependent antiviral IFN responses in target macrophages and protection from HIV infection...
October 12, 2016: Cell Host & Microbe
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