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Horizontal DNA transfer

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https://www.readbyqxmd.com/read/29778228/the-highly-heterogeneous-methylated-genomes-and-diverse-restriction-modification-systems-of-bloom-forming-microcystis
#1
Liang Zhao, Yulong Song, Lin Li, Nanqin Gan, Jerry J Brand, Lirong Song
The occurrence of harmful Microcystis blooms is increasing in frequency in a myriad of freshwater ecosystems. Despite considerable research pertaining to the cause and nature of these blooms, the molecular mechanisms behind the cosmopolitan distribution and phenotypic diversity in Microcystis are still unclear. We compared the patterns and extent of DNA methylation in three strains of Microcystis, PCC 7806SL, NIES-2549 and FACHB-1757, using Single Molecule Real-Time (SMRT) sequencing technology. Intact restriction-modification (R-M) systems were identified from the genomes of these strains, and from two previously sequenced strains of Microcystis, NIES-843 and TAIHU98...
May 2018: Harmful Algae
https://www.readbyqxmd.com/read/29769342/cotesia-congregata-bracovirus-circles-encoding-ptp-and-ankyrin-genes-integrate-into-the-dna-of-parasitized-manduca-sexta-hemocytes
#2
Germain Chevignon, Georges Periquet, Gabor Gyapay, Nathalie Vega-Czarny, Karine Musset, Jean-Michel Drezen, Elisabeth Huguet
Polydnaviruses (PDVs) are essential for the parasitism success of tens of thousands of species of parasitoid wasps. PDVs are present in wasp genomes as proviruses, which serve as template for the production of double stranded circular viral DNA carrying virulence genes that are injected into lepidopteran hosts. PDV circles do not contain genes coding for particle production hence impeding viral replication in caterpillar hosts during parasitism. Here we investigated the fate of PDV circles of Cotesia congregata bracovirus during parasitism of the tobacco hornworm, Manduca sexta , by the wasp Cotesia congregata Sequences sharing similarities with Host integration Motifs (HIM) involved in integration into DNA of Microplitis demolitor bracovirus (MdBV) circles, could be identified in 12 CcBV circles, which encode PTP and VANK gene families involved in host immune disruption...
May 16, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29760209/complex-control-of-a-genomic-island-governing-biofilm-and-rugose-colony-development-in-vibrio-vulnificus
#3
Daniel M Chodur, Dean A Rowe-Magnus
V. vulnificus is a potent opportunistic human pathogen that contaminates the human food-chain by asymptomatically colonizing seafood. Expression of the 9-gene brp exopolysaccharide locus mediates surface adherence and is controlled by the secondary signaling molecule c-di-GMP and the regulator BrpT. Here, we show that c-di-GMP and BrpT also regulate the expression of an adjacent 5-gene cluster that includes the cabABC operon, brpT and another VpsT-like transcriptional regulator, brpS The expression of the 14 genes spanning the region increased with elevated intracellular c -di-GMP levels in a BrpT-dependent manner, save brpS , which was positively regulated by c-di-GMP and repressed by BrpT...
May 14, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29751066/keeping-it-together-absence-of-genetic-variation-and-dna-incorporation-by-the-predatory-bacteria-micavibrio-aeruginosavorus-and-bdellovibrio-bacteriovorus-during-predation
#4
Shilpi Gupta, Alexander Lemenze, Robert J Donnelly, Nancy D Connell, Daniel E Kadouri
The use of predatory bacteria as a potential live therapeutic to control human infection is gaining increased attention. Earlier work with Micavibrio spp. and Bdellovibrio spp. has demonstrated the ability of these predators to control drug-resistant Gram-negative pathogens, Tier-1 select agents and biofilms. Additional studies also confirmed that introducing high doses of the predators into animals does not negatively impact animal well-being and might assist in reducing bacterial burden in vivo. The survival of predators requires extreme proximity to the prey cell, which might bring about horizontal transfer of genetic material, such as genes encoding for pathogenic genetic islands that would indirectly facilitate the spread of genetic material to other organisms...
May 8, 2018: Research in Microbiology
https://www.readbyqxmd.com/read/29733586/the-biphenyl-metabolizing-microbial-community-and-a-functional-operon-revealed-in-e-waste-contaminated-soil
#5
Longfei Jiang, Chunling Luo, Dayi Zhang, Mengke Song, Yingtao Sun, Gan Zhang
Primitive electronic waste (e-waste) recycling activities release massive amounts of persistent organic pollutants (POPs) and heavy metals into surrounding soils, posing a major threat to the ecosystem and human health. Microbes capable of metabolizing POPs play important roles in POPs remediation in soils, but their phylotypes and functions remain unclear. Polychlorinated biphenyls (PCBs), one of the main pollutants in e-waste contaminated soils, have drawn increasing attention due to their high persistence, toxicity, and bioaccumulation...
May 7, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29724163/eugi-a-novel-resource-for-studying-genomic-islands-to-facilitate-horizontal-gene-transfer-detection-in-eukaryotes
#6
Frederick Johannes Clasen, Rian Ewald Pierneef, Bernard Slippers, Oleg Reva
BACKGROUND: Genomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT). There are evidences that GIs can contribute significantly to the evolution of prokaryotes. The acquisition of GIs through HGT in eukaryotes has, however, been largely unexplored. In this study, the previously developed GI prediction tool, SeqWord Gene Island Sniffer (SWGIS), is modified to predict GIs in eukaryotic chromosomes. Artificial simulations are used to estimate ratios of predicting false positive and false negative GIs by inserting GIs into different test chromosomes and performing the SWGIS v2...
May 3, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29723434/prgb-promotes-aggregation-biofilm-formation-and-conjugation-through-dna-binding-and-compaction
#7
Andreas Schmitt, Kai Jiang, Martha I Camacho, Venkateswara Rao Jonna, Anders Hofer, Fredrik Westerlund, Peter J Christie, Ronnie P-A Berntsson
Gram-positive bacteria deploy type IV secretion systems (T4SSs) to facilitate horizontal gene transfer. The T4SSs of Gram-positive bacteria rely on surface adhesins as opposed to conjugative pili to facilitate mating. Enterococcus faecalis PrgB is a surface adhesin that promotes mating pair formation and robust biofilm development in an extracellular DNA (eDNA) dependent manner. Here we report the structure of the adhesin domain of PrgB. The adhesin domain binds and compacts DNA in vitro. In vivo PrgB deleted of its adhesin domain does not support cellular aggregation, biofilm development and conjugative DNA transfer...
May 3, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29722872/comm-is-a-hexameric-helicase-that-promotes-branch-migration-during-natural-transformation-in-diverse-gram-negative-species
#8
Thomas M Nero, Triana N Dalia, Joseph Che-Yen Wang, David T Kysela, Matthew L Bochman, Ankur B Dalia
Acquisition of foreign DNA by natural transformation is an important mechanism of adaptation and evolution in diverse microbial species. Here, we characterize the mechanism of ComM, a broadly conserved AAA+ protein previously implicated in homologous recombination of transforming DNA (tDNA) in naturally competent Gram-negative bacterial species. In vivo, we found that ComM was required for efficient comigration of linked genetic markers in Vibrio cholerae and Acinetobacter baylyi, which is consistent with a role in branch migration...
May 2, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29717025/the-type-iv-pilus-assembly-motor-pilb-is-a-robust-hexameric-atpase-with-complex-kinetics
#9
Andreas Sukmana, Zhaomin Yang
The bacterial type IV pilus (T4P) is a versatile nanomachine that functions in pathogenesis, biofilm formation, motility, and horizontal gene transfer. T4P assembly is powered by the motor ATPase PilB which is proposed to hydrolyze ATP by a symmetrical rotary mechanism. This mechanism, which is deduced from the structure of PilB, is untested. Here, we report the first kinetic studies of the PilB ATPase, supporting coordination among the protomers of this hexameric enzyme. Analysis of the genome sequence of Chloracidobacterium thermophilum identified a pilB gene whose protein we then heterologously expressed...
May 1, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29717009/an-attenuated-crispr-cas-system-in-enterococcus-faecalis-permits-dna-acquisition
#10
Karthik Hullahalli, Marinelle Rodrigues, Uyen Thy Nguyen, Kelli Palmer
Antibiotic-resistant bacteria are critical public health concerns. Among the prime causative factors for the spread of antibiotic resistance is horizontal gene transfer (HGT). A useful model organism for investigating the relationship between HGT and antibiotic resistance is the opportunistic pathogen Enterococcus faecalis , since the species possesses highly conjugative plasmids that readily disseminate antibiotic resistance genes and virulence factors in nature. Unlike many commensal E. faecalis strains, the genomes of multidrug-resistant (MDR) E...
May 1, 2018: MBio
https://www.readbyqxmd.com/read/29695294/the-hologenome-concept-of-evolution-after-10-years
#11
REVIEW
Eugene Rosenberg, Ilana Zilber-Rosenberg
The holobiont (host with its endocellular and extracellular microbiome) can function as a distinct biological entity, an additional organismal level to the ones previously considered, on which natural selection operates. The holobiont can function as a whole: anatomically, metabolically, immunologically, developmentally, and during evolution. Consideration of the holobiont with its hologenome as an independent level of selection in evolution has led to a better understanding of underappreciated modes of genetic variation and evolution...
April 25, 2018: Microbiome
https://www.readbyqxmd.com/read/29673327/assessing-the-benefits-of-horizontal-gene-transfer-by-laboratory-evolution-and-genome-sequencing
#12
Hoi Yee Chu, Kathleen Sprouffske, Andreas Wagner
BACKGROUND: Recombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits. In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. While such transfer is widespread in natural communities, its immediate fitness benefits are usually unknown. We asked whether any such benefits depend on the environment, and on the identity of donor and recipient strains. To this end, we adapted Escherichia coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors...
April 19, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29670105/viral-proteins-as-a-potential-driver-of-histone-depletion-in-dinoflagellates
#13
Nicholas A T Irwin, Benjamin J E Martin, Barry P Young, Martin J G Browne, Andrew Flaus, Christopher J R Loewen, Patrick J Keeling, LeAnn J Howe
Within canonical eukaryotic nuclei, DNA is packaged with highly conserved histone proteins into nucleosomes, which facilitate DNA condensation and contribute to genomic regulation. Yet the dinoflagellates, a group of unicellular algae, are a striking exception to this otherwise universal feature as they have largely abandoned histones and acquired apparently viral-derived substitutes termed DVNPs (dinoflagellate-viral-nucleoproteins). Despite the magnitude of this transition, its evolutionary drivers remain unknown...
April 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29669918/horizontal-transfer-of-retrotransposons-between-bivalves-and-other-aquatic-species-of-multiple-phyla
#14
Michael J Metzger, Ashley N Paynter, Mark E Siddall, Stephen P Goff
The LTR retrotransposon Steamer is a selfish endogenous element in the soft-shell clam genome that was first detected because of its dramatic amplification in bivalve transmissible neoplasia afflicting the species. We amplified and sequenced related retrotransposons from the genomic DNA of many other bivalve species, finding evidence of horizontal transfer of retrotransposons from the genome of one species to another. First, the phylogenetic tree of the Steamer -like elements from 19 bivalve species is markedly discordant with host phylogeny, suggesting frequent cross-species transfer throughout bivalve evolution...
April 18, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29669186/blending-genomes-distributive-conjugal-transfer-in-mycobacteria-a-sexier-form-of-hgt
#15
REVIEW
Todd A Gray, Keith M Derbyshire
This review discusses a novel form of horizontal gene transfer (HGT) found in mycobacteria called Distributive Conjugal Transfer (DCT). While satisfying the criteria for conjugation, DCT occurs by a mechanism so distinct from oriT-mediated conjugation that it could be considered a fourth category of HGT. DCT involves the transfer of chromosomal DNA between mycobacteria and, most significantly, generates transconjugants with mosaic genomes of the parental strains. Multiple segments of donor chromosomal DNA can be co-transferred regardless of their location or the genetic selection and, as a result, the transconjugant genome contains many donor-derived segments; hence the name DCT...
April 18, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29666765/characterization-of-antimicrobial-resistance-genes-in-haemophilus-parasuis-isolated-from-pigs-in-china
#16
Yongda Zhao, Lili Guo, Jie Li, Xianhui Huang, Binghu Fang
Background: Haemophilus parasuis is a common porcine respiratory pathogen that causes high rates of morbidity and mortality in farmed swine. We performed a molecular characterization of antimicrobial resistance genes harbored by H. parasuis from pig farms in China. Methods: We screened 143 H. parasuis isolates for antimicrobial susceptibility against six fluoroquinolone antibiotics testing by the broth microdilution method, and the presence of 64 antimicrobial resistance genes by PCR amplification and DNA sequence analysis...
2018: PeerJ
https://www.readbyqxmd.com/read/29665884/factors-influencing-horizontal-gene-transfer-in-the-intestine
#17
Ximin Zeng, Jun Lin
Antibiotic resistance (AR) is ancient. Use of antibiotics is a selective driving force that enriches AR genes and promotes the emergence of resistant pathogens. It also has been widely accepted that horizontal gene transfer (HGT) occurs everywhere and plays a critical role in the transmission of AR genes among bacteria. However, our understanding of HGT processes primarily build on extensive in vitro studies; to date, there is still a significant knowledge gap regarding in situ HGT events as well as the factors that influence HGT in different ecological niches...
December 2017: Animal Health Research Reviews
https://www.readbyqxmd.com/read/29659762/activation-of-%C3%AF-20-dependent-recombination-and-horizontal-gene-transfer-in-mycoplasma-genitalium
#18
Sergi Torres-Puig, Carlos Martínez-Torró, Ignasi Granero-Moya, Enrique Querol, Jaume Piñol, Oscar Q Pich
In the human pathogen Mycoplasma genitalium, homologous recombination is under the control of σ20, an alternative sigma factor that boosts the generation of genetic and antigenic diversity in the population. Under laboratory growth conditions, σ20 activation is rare and the factors governing its intermittent activity are unknown. Two σ20-regulated genes, rrlA and rrlB, showed to be important for recombination of homologous DNA sequences in this bacterium. Herein, we demonstrate that rrlA and rrlB code for two small proteins that participate in a feed-forward loop essential for σ20 function...
April 11, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29648539/horizontal-gene-transfer-in-thermus-spp
#19
Alba Blesa, Beate Averhoff, José Berenguer
The small amount of genetic content in thermophiles generally limits their adaptability to environmental changes. In Thermus spp., very active horizontal gene transfer (HGT) mechanisms allow the rapid spread of strain-specific adaptive gene modules among the entire population. Constitutive expression of a rather particular and highly efficient DNA transport apparatus (DTA) is at the center of this HGT-mediated enhanced adaptability. The function of the DTA is dependent on the integrity and longevity of the extracellular DNA (eDNA) being transformed, which can be improved by the production of extracellular vesicles (EV) through lysis of a fraction of the population...
April 12, 2018: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/29625982/the-protease-clpxp-and-the-pas-domain-protein-divl-regulate-ctra-and-gene-transfer-agent-production-in-rhodobacter-capsulatus
#20
A B Westbye, L Kater, C Wiesmann, H Ding, C K Yip, J T Beatty
Several members of the Rhodobacterales ( Alphaproteobacteria ) produce a conserved horizontal gene transfer vector, called gene transfer agent (GTA), that appears to have evolved from a bacteriophage. The model system to study GTA biology is the R. capsulatus GTA (RcGTA), a small, tailed bacteriophage-like particle produced by a subset of the cells in a culture. The response regulator CtrA is conserved in the Alphaproteobacteria and is an essential regulator of RcGTA production: it controls production and maturation of the RcGTA particle and RcGTA release from cells...
April 6, 2018: Applied and Environmental Microbiology
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