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Horizontal DNA transfer

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https://www.readbyqxmd.com/read/28912766/environmental-bacteriophages-of-the-emerging-enterobacterial-phytopathogen-dickeya-solani-show-genomic-conservation-and-capacity-for-horizontal-gene-transfer-between-their-bacterial-hosts
#1
Andrew Day, Jiyoon Ahn, Xinzhe Fang, George P C Salmond
Dickeya solani is an economically important phytopathogen widespread in mainland Europe that can reduce potato crop yields by 25%. There are no effective environmentally-acceptable chemical systems available for diseases caused by Dickeya. Bacteriophages have been suggested for use in biocontrol of this pathogen in the field, and limited field trials have been conducted. To date only a small number of bacteriophages capable of infecting D. solani have been isolated and characterized, and so there is a need to expand the repertoire of phages that may have potential utility in phage therapy strategies...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28911112/integrative-and-conjugative-elements-and-their-hosts-composition-distribution-and-organization
#2
Jean Cury, Marie Touchon, Eduardo P C Rocha
Conjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species' pan-genome...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28871175/fluorescent-crispr-adaptation-reporter-for-rapid-quantification-of-spacer-acquisition
#3
Lina Amlinger, Mirthe Hoekzema, E Gerhart H Wagner, Sanna Koskiniemi, Magnus Lundgren
CRISPR-Cas systems are adaptive prokaryotic immune systems protecting against horizontally transferred DNA or RNA such as viruses and other mobile genetic elements. Memory of past invaders is stored as spacers in CRISPR loci in a process called adaptation. Here we developed a novel assay where spacer integration results in fluorescence, enabling detection of memory formation in single cells and quantification of as few as 0.05% cells with expanded CRISPR arrays in a bacterial population. Using this fluorescent CRISPR Adaptation Reporter (f-CAR), we quantified adaptation of the two CRISPR arrays of the type I-E CRISPR-Cas system in Escherichia coli, and confirmed that more integration events are targeted to CRISPR-II than to CRISPR-I...
September 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28864953/monitoring-of-genetically-modified-escherichia-coli-in-laboratory-wastewater
#4
Fabienne Wichmann, Ines Wyrsch, Jörg Frank, Matthias Müller, Nicole Bertschi, Peter Brodmann, Claudia Bagutti
Containment of genetically modified (GM) microorganisms such as Escherichia coli is a legal requirement to protect the environment from an unintended release and to avoid horizontal gene transfer (HGT) of recombinant DNA to native bacteria. In this study, we sampled the laboratory wastewater (LWW) at a large Swiss university from three sources over 2 years and cultured ampicillin-resistant, presumptive GM E. coli. From a total of 285 samples, 127 contained presumptive GM E. coli (45%) at a mean concentration of 2...
September 1, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28859885/case-studies-on-genetically-modified-organisms-gmos-potential-risk-scenarios-and-associated-health-indicators
#5
Barbara De Santis, Norbert Stockhofe, Jean-Michel Wal, Eefke Weesendorp, Jean Paul Lallès, Jeroen van Dijk, Esther Kok, Marzia De Giacomo, Ralf Einspanier, Roberta Onori, Carlo Brera, Paul Bikker, Jan van der Meulen, Kleter Gijs
Within the frame of the EU-funded MARLON project, background data were reviewed to explore the possibility of measuring health indicators during post-market monitoring for potential effects of feeds, particularly genetically modified (GM) feeds, on livestock animal health, if applicable. Four case studies (CSs) of potential health effects on livestock were framed and the current knowledge of a possible effect of GM feed was reviewed. Concerning allergenicity (CS-1), there are no case-reports of allergic reactions or immunotoxic effects resulting from GM feed consumption as compared with non-GM feed...
August 28, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28854875/xanthomonas-adaptation-to-common-bean-is-associated-with-horizontal-transfers-of-genes-encoding-tal-effectors
#6
Mylène Ruh, Martial Briand, Sophie Bonneau, Marie-Agnès Jacques, Nicolas W G Chen
BACKGROUND: Common bacterial blight is a devastating bacterial disease of common bean (Phaseolus vulgaris) caused by Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli. These phylogenetically distant strains are able to cause similar symptoms on common bean, suggesting that they have acquired common genetic determinants of adaptation to common bean. Transcription Activator-Like (TAL) effectors are bacterial type III effectors that are able to induce the expression of host genes to promote infection or resistance...
August 30, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28839913/biological-action-in-read-write-genome-evolution
#7
REVIEW
James A Shapiro
Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals...
October 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/28839126/ancestor-of-land-plants-acquired-the-dna-3-methyladenine-glycosylase-mag-gene-from-bacteria-through-horizontal-gene-transfer
#8
Huimin Fang, Liexiang Huangfu, Rujia Chen, Pengcheng Li, Shuhui Xu, Enying Zhang, Wei Cao, Li Liu, Youli Yao, Guohua Liang, Chenwu Xu, Yong Zhou, Zefeng Yang
The origin and evolution of land plants was an important event in the history of life and initiated the establishment of modern terrestrial ecosystems. From water to terrestrial environments, plants needed to overcome the enhanced ultraviolet (UV) radiation and many other DNA-damaging agents. Evolving new genes with the function of DNA repair is critical for the origin and radiation of land plants. In bacteria, the DNA-3-methyladenine glycosylase (MAG) recognizes of a variety of base lesions and initiates the process of the base excision repair for damaged DNA...
August 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28802274/horizontal-dissemination-of-antimicrobial-resistance-determinants-in-multiple-salmonella-serotypes-following-isolation-from-the-environment-of-commercial-swine-operations-after-manure-application
#9
Suchawan Pornsukarom, Siddhartha Thakur
The aim of this study was to characterize the plasmids carrying antimicrobial resistance (AMR) determinants in multiple Salmonella serotypes recovered from the commercial swine farms environment after manure application on land. Manure and soil samples were collected on day0 before and after manure application on six farms in North Carolina and sequential soil samples were recollected on day7, 14, and 21 from the same plots. All environmental samples were processed for Salmonella and their plasmid contents were further characterized...
August 11, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28793862/physical-shearing-imparts-biological-activity-to-dna-and-ability-to-transmit-itself-horizontally-across-species-and-kingdom-boundaries
#10
Gorantla Venkata Raghuram, Deepika Gupta, Siddharth Subramaniam, Ashwini Gaikwad, Naveen Kumar Khare, Malcolm Nobre, Naveen Kumar Nair, Indraneel Mittra
BACKGROUND: We have recently reported that cell-free DNA (cfDNA) fragments derived from dying cells that circulate in blood are biologically active molecules and can readily enter into healthy cells to activate DNA damage and apoptotic responses in the recipients. However, DNA is not conventionally known to spontaneously enter into cells or to have any intrinsic biological activity. We hypothesized that cellular entry and acquisition of biological properties are functions of the size of DNA...
August 9, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28790994/insight-into-the-origin-and-evolution-of-the-vibrio-parahaemolyticus-pandemic-strain
#11
REVIEW
Romilio T Espejo, Katherine García, Nicolas Plaza
A strain of Vibrio parahaemolyticus that emerged in 1995 caused the first known pandemic involving this species. This strain comprises clonal autochthonous ocean-dwelling bacteria whose evolution has occurred in the ocean environment. The low sequence diversity in this population enabled the discovery of information on its origin and evolution that has been hidden in bacterial clones that have evolved over a long period. Multilocus sequencing and microarray analysis, together with phylogenetic analysis, of pandemic and pre-pandemic isolates has suggested that the founder clone was an O3:K6 non-pathogenic strain that initially acquired a toxRS/new region and subsequently acquired at least seven novel genomic islands...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28743812/horizontal-gene-transfer-of-functional-type-vi-killing-genes-by-natural-transformation
#12
Jacob Thomas, Samit S Watve, William C Ratcliff, Brian K Hammer
Horizontal gene transfer (HGT) can have profound effects on bacterial evolution by allowing individuals to rapidly acquire adaptive traits that shape their strategies for competition. One strategy for intermicrobial antagonism often used by Proteobacteria is the genetically encoded contact-dependent type VI secretion system (T6SS), a weapon used to kill heteroclonal neighbors by direct injection of toxic effectors. Here, we experimentally demonstrate that Vibrio cholerae can acquire new T6SS effector genes via horizontal transfer and utilize them to kill neighboring cells...
July 25, 2017: MBio
https://www.readbyqxmd.com/read/28732043/investigation-of-horizontal-gene-transfer-of-pathogenicity-islands-in-escherichia-coli-using-next-generation-sequencing
#13
Maxim Messerer, Wolfgang Fischer, Sören Schubert
Horizontal gene transfer (HGT) contributes to the evolution of bacteria. All extraintestinal pathogenic Escherichia coli (ExPEC) harbour pathogenicity islands (PAIs), however relatively little is known about the acquisition of these PAIs. Due to these islands, ExPEC have properties to colonize and invade its hosts efficiently. Even though these PAIs are known to be acquired by HGT, only very few PAIs do carry mobilization and transfer genes required for the transmission by HGT. In this study, we apply for the first time next-generation sequencing (NGS) and in silico analyses in combination with in vitro experiments to decipher the mechanisms of PAI acquisition in ExPEC...
2017: PloS One
https://www.readbyqxmd.com/read/28720902/comparative-genomic-analysis-of-paenibacillus-sp-ssg-1-and-its-closely-related-strains-reveals-the-effect-of-glycometabolism-on-environmental-adaptation
#14
Hui Xu, Shishang Qin, Yanhong Lan, Mengjia Liu, Xiyue Cao, Dairong Qiao, Yu Cao, Yi Cao
The extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28706512/comparative-genomics-reveals-high-genomic-diversity-in-the-genus-photobacterium
#15
Henrique Machado, Lone Gram
Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28698278/on-the-origin-of-reverse-transcriptase-using-crispr-cas-systems-and-their-hyperdiverse-enigmatic-spacer-repertoires
#16
Sukrit Silas, Kira S Makarova, Sergey Shmakov, David Páez-Espino, Georg Mohr, Yi Liu, Michelle Davison, Simon Roux, Siddharth R Krishnamurthy, Becky Xu Hua Fu, Loren L Hansen, David Wang, Matthew B Sullivan, Andrew Millard, Martha R Clokie, Devaki Bhaya, Alan M Lambowitz, Nikos C Kyrpides, Eugene V Koonin, Andrew Z Fire
Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains...
July 11, 2017: MBio
https://www.readbyqxmd.com/read/28683561/ros-mediated-autophagy-defines-the-fate-of-cancer-stem-cells
#17
Matilde E Lleonart, Etna Abad, Dmitry Graifer, Alex Lyakhovich
SIGNIFICANCE: A fraction of tumorigenic cells, also known as tumor initiating or cancer stem cells, is thought to drive tumor growth, metastasis and chemoresistance. However, little is known regarding mechanisms that convey relevant pathways contributing to their self-renewal, proliferation and differentiation abilities. Recent Advances: Recent works on cancer stem cells provide evidence on the role of redox disruption and regulation of autophagic flux. This has been linked to increased DNA repair capacity and chemoresistance...
July 6, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28683122/the-nucleoid-occlusion-protein-slma-is-a-direct-transcriptional-activator-of-chitobiose-utilization-in-vibrio-cholerae
#18
Catherine A Klancher, Chelsea A Hayes, Ankur B Dalia
Chitin utilization by the cholera pathogen Vibrio cholerae is required for its persistence and evolution via horizontal gene transfer in the marine environment. Genes involved in the uptake and catabolism of the chitin disaccharide chitobiose are encoded by the chb operon. The orphan sensor kinase ChiS is critical for regulation of this locus, however, the mechanisms downstream of ChiS activation that result in expression of the chb operon are poorly understood. Using an unbiased transposon mutant screen, we uncover that the nucleoid occlusion protein SlmA is a regulator of the chb operon...
July 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28682556/-the-origin-of-hydrogen-peroxide-in-oral-cavity-and-its-role-in-oral-microecology-balance
#19
Zhang Keke, Zhou Xuedong, Xu Xin
Hydrogen peroxide, an important antimicrobial agent in oral cavity, plays a significant role in the balance of oral microecology. At the early stage of biofilm formation, about 80% of the detected initial colonizers belong to the genus Streptococcus. These oral streptococci use different oxidase to produce hydrogen peroxide. Recent studies showed that the produced hydrogen peroxide plays a critical role in modulating oral microecology. Hydrogen peroxide modulates biofilm development attributed to its growth inhibitory nature...
April 1, 2017: Hua Xi Kou Qiang Yi Xue za Zhi, Huaxi Kouqiang Yixue Zazhi, West China Journal of Stomatology
https://www.readbyqxmd.com/read/28676809/phylogenomic-analysis-and-dynamic-evolution-of-chloroplast-genomes-in-salicaceae
#20
Yuan Huang, Jun Wang, Yongping Yang, Chuanzhu Fan, Jiahui Chen
Chloroplast genomes of plants are highly conserved in both gene order and gene content. Analysis of the whole chloroplast genome is known to provide much more informative DNA sites and thus generates high resolution for plant phylogenies. Here, we report the complete chloroplast genomes of three Salix species in family Salicaceae. Phylogeny of Salicaceae inferred from complete chloroplast genomes is generally consistent with previous studies but resolved with higher statistical support. Incongruences of phylogeny, however, are observed in genus Populus, which most likely results from homoplasy...
2017: Frontiers in Plant Science
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