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Horizontal DNA transfer

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https://www.readbyqxmd.com/read/28104347/bacterial-resistance-to-antibodies-a-model-evolutionary-study
#1
Lawrence S Schulman
The tangled nature model of evolution (reviewed in the main text) is adapted for use in the study of antibody resistance acquired by horizontal gene transfer. Exchanges of DNA and the acquisition of resistant gene sequences are considered. For the parameters used, resistant strains rapidly proliferate and dominate, although initial intense antibiotic treatment can occasionally prevent this. Variation in genome distribution appears to be long tailed. If this is reflected in nature, the occurrence of resistant bacterial strains can be expected, as well as considerable variation in patient outcomes...
January 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28096488/novel-superspreader-bacteriophages-promote-horizontal-gene-transfer-by-transformation
#2
Eric C Keen, Valery V Bliskovsky, Francisco Malagon, James D Baker, Jeffrey S Prince, James S Klaus, Sankar L Adhya
: Bacteriophages infect an estimated 10(23) to 10(25) bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub "superspreaders," releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096446/the-rpn-yhga-like-proteins-of-escherichia-coli-k-12-and-their-contribution-to-reca-independent-horizontal-transfer
#3
Anthony W Kingston, Christine Ponkratz, Elisabeth A Raleigh
: Bacteria use a variety of DNA mobilizing enzymes to facilitate environmental niche adaptation via horizontal gene transfer. This has led to real world problems, like the spread of antibiotic resistance, yet many mobilization proteins remain undefined. Here, we investigate the uncharacterized family of YhgA-like "transposase_31" proteins (PF04754). Our primary focus was the genetic and biochemical properties of the five E. coli K-12 members of this family, which we designate RpnA-RpnE for recombination promoting nuclease...
January 17, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28077296/extracellular-vesicle-communication-pathways-as-regulatory-targets-of-oncogenic-transformation
#4
REVIEW
Dongsic Choi, Tae Hoon Lee, Cristiana Spinelli, Shilpa Chennakrishnaiah, Esterina D'Asti, Janusz Rak
Pathogenesis of human cancers bridges intracellular oncogenic driver events and their impact on intercellular communication. Among multiple mediators of this 'pathological connectivity' the role of extracellular vesicles (EVs) and their subsets (exosomes, ectosomes, oncosomes) is of particular interest for several reasons. The release of EVs from cancer cells represents a unique mechanism of regulated expulsion of bioactive molecules, a process that also mediates cell-to-cell transfer of lipids, proteins, and nucleic acids...
January 8, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28067866/horizontally-acquired-at-rich-genes-in-escherichia-coli-cause-toxicity-by-sequestering-rna-polymerase
#5
Lisa E Lamberte, Gabriele Baniulyte, Shivani S Singh, Anne M Stringer, Richard P Bonocora, Mathew Stracy, Achillefs N Kapanidis, Joseph T Wade, David C Grainger
Horizontal gene transfer permits rapid dissemination of genetic elements between individuals in bacterial populations. Transmitted DNA sequences may encode favourable traits. However, if the acquired DNA has an atypical base composition, it can reduce host fitness. Consequently, bacteria have evolved strategies to minimize the harmful effects of foreign genes. Most notably, xenogeneic silencing proteins bind incoming DNA that has a higher AT content than the host genome. An enduring question has been why such sequences are deleterious...
January 9, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28067311/supra-operonic-clusters-of-functionally-related-genes-socs-are-a-source-of-horizontal-gene-co-transfers
#6
Tin Yau Pang, Martin J Lercher
Adaptation of bacteria occurs predominantly via horizontal gene transfer (HGT). While it is widely recognized that horizontal acquisitions frequently encompass multiple genes, it is unclear what the size distribution of successfully transferred DNA segments looks like and what evolutionary forces shape this distribution. Here, we identified 1790 gene family pairs that were consistently co-gained on the same branches across a phylogeny of 53 E. coli strains. We estimated a lower limit of their genomic distances at the time they were transferred to their host genomes; this distribution shows a sharp upper bound at 30 kb...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28047053/we-h-bra-06-experimental-investigation-of-rbe-for-lung-cancer-cell-lines-as-a-function-of-dose-and-let-in-proton-helium-and-carbon-beams
#7
D Patel, L Bronk, F Guan, C Peeler, D Mirkovic, D Grosshans, O Jakel, A Abdollahi, U Titt, R Mohan
PURPOSE: Investigate and quantify the effect of dose and LET on the RBE of protons, helium and carbon ions. METHODS: High throughput, high accuracy experimental setups were custom designed to investigate the Relative Biological Effectiveness (RBE) dependence on the dose and Linear Energy Transfer (LET) values for proton, helium and carbon ion beams. The experiment was conducted at the HIT facility in collaboration with the DKFZ in Heidelberg/Germany. Clonogenic assays of two human lung cancer cell lines, H460 and H1437, were investigated in this study...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28024527/in-silico-prediction-of-dual-function-of-dksa-like-hypothetical-protein-in-v-cholerae-o395-genome
#8
Avirup Dutta, Atul Katarkar, Keya Chaudhuri
Cholera, an acute infection of the small intestine, is caused by Vibrio cholerae. The present study identified a hypothetical protein in V. cholerae O395, which was predicted to be acquired through horizontal gene transfer the origin of which was found to be from a phage. Its expression was further confirmed by RT-PCR. Homology based 3D model of the hypothetical protein indicated DksA like homologue. Protein binding site of 3D-model revealed a deep cleft which may influence the dimer formation and interaction with ds-DNA molecule...
January 2017: Microbiological Research
https://www.readbyqxmd.com/read/27999570/gene-turnover-contributes-to-the-evolutionary-adaptation-of-acidithiobacillus-caldus-insights-from-comparative-genomics
#9
Xian Zhang, Xueduan Liu, Qiang He, Weiling Dong, Xiaoxia Zhang, Fenliang Fan, Deliang Peng, Wenkun Huang, Huaqun Yin
Acidithiobacillus caldus is an extremely acidophilic sulfur-oxidizer with specialized characteristics, such as tolerance to low pH and heavy metal resistance. To gain novel insights into its genetic complexity, we chosen six A. caldus strains for comparative survey. All strains analyzed in this study differ in geographic origins as well as in ecological preferences. Based on phylogenomic analysis, we clustered the six A. caldus strains isolated from various ecological niches into two groups: group 1 strains with smaller genomes and group 2 strains with larger genomes...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27979968/rag-recombinase-as-a-selective-pressure-for-genome-evolution
#10
D Passagem-Santos, M Bonnet, D Sobral, I Trancoso, J G Silva, V M Barreto, A Athanasiadis, J Demengeot, J B Pereira-Leal
The RAG recombinase is a domesticated transposable element co-opted in jawed vertebrates to drive the process of the so-called V(D)J recombination, which is the hallmark of the adaptive immune system to produce antigen receptors. RAG targets, namely, the Recombination Signal Sequences (RSS), are rather long and degenerated sequences, which highlights the ability of the recombinase to interact with a wide range of target sequences, including outside of antigen receptor loci. The recognition of such cryptic targets by the recombinase threatens genome integrity by promoting aberrant DNA recombination, as observed in lymphoid malignancies...
December 14, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27975296/erratum-to-the-type-i-restriction-enzymes-as-barriers-to-horizontal-gene-transfer-determination-of-the-dna-target-sequences-recognised-by-livestock-associated-methicillin-resistant-staphylococcus-aureus-clonal-complexes-133-st771-and-398
#11
Kai Chen, Augoustinos S Stephanou, Gareth A Roberts, John H White, Laurie P Cooper, Patrick J Houston, Jodi A Lindsay, David T F Dryden
No abstract text is available yet for this article.
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27965650/an-integrative-genomic-island-affects-the-adaptations-of-the-piezophilic-hyperthermophilic-archaeon-pyrococcus-yayanosii-to-high-temperature-and-high-hydrostatic-pressure
#12
Zhen Li, Xuegong Li, Xiang Xiao, Jun Xu
Deep-sea hydrothermal vent environments are characterized by high hydrostatic pressure and sharp temperature and chemical gradients. Horizontal gene transfer is thought to play an important role in the microbial adaptation to such an extreme environment. In this study, a 21.4-kb DNA fragment was identified as a genomic island, designated PYG1, in the genomic sequence of the piezophilic hyperthermophile Pyrococcus yayanosii. According to the sequence alignment and functional annotation, the genes in PYG1 could tentatively be divided into five modules, with functions related to mobility, DNA repair, metabolic processes and the toxin-antitoxin system...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27956618/substitutions-of-short-heterologous-dna-segments-of-intragenomic-or-extragenomic-origins-produce-clustered-genomic-polymorphisms
#13
Klaus Harms, Asbjørn Lunnan, Nils Hülter, Tobias Mourier, Lasse Vinner, Cheryl P Andam, Pekka Marttinen, Helena Fridholm, Anders Johannes Hansen, William P Hanage, Kaare Magne Nielsen, Eske Willerslev, Pål Jarle Johnsen
In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi...
December 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27956257/a-report-on-extensive-lateral-genetic-reciprocation-between-arsenic-resistant-bacillus-subtilis-and-bacillus-pumilus-strains-analyzed-using-rapd-pcr
#14
Sapna Khowal, Md Zulquarnain Siddiqui, Shadab Ali, Mohd Taha Khan, Mather Ali Khan, Samar Husain Naqvi, Saima Wajid
The study involves isolation of arsenic resistant bacteria from soil samples. The characterization of bacteria isolates was based on 16S rRNA gene sequences. The phylogenetic consanguinity among isolates was studied employing rpoB and gltX gene sequence. RAPD-PCR technique was used to analyze genetic similarity between arsenic resistant isolates. In accordance with the results Bacillus subtilis and Bacillus pumilus strains may exhibit extensive horizontal gene transfer. Arsenic resistant potency in Bacillus sonorensis and high arsenite tolerance in Bacillus pumilus strains was identified...
December 10, 2016: Molecular Phylogenetics and Evolution
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
#15
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...
January 2017: 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
#16
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...
February 2017: 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
#17
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
#18
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
#19
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
#20
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...
January 9, 2017: Nucleic Acids Research
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