keyword
MENU ▼
Read by QxMD icon Read
search

Transposons

keyword
https://www.readbyqxmd.com/read/28101896/adaptation-of-genetically-monomorphic-bacteria-evolution-of-copper-resistance-through-multiple-horizontal-gene-transfers-of-complex-and-versatile-mobile-genetic-elements
#1
D Richard, V Ravigné, A Rieux, B Facon, C Boyer, K Boyer, P Grygiel, S Javegny, M Terville, B I Canteros, I Robène, C Vernière, A Chabirand, O Pruvost, P Lefeuvre
Copper-based antimicrobial compounds are widely used to control plant bacterial pathogens. Pathogens have adapted in response to this selective pressure. Xanthomonas citri pv. citri, a major citrus pathogen causing Asiatic citrus canker, was first reported to carry plasmid-encoded copper resistance in Argentina. This phenotype was conferred by the copLAB gene system. The emergence of resistant strains has since been reported in Réunion and Martinique. Using microsatellite-based genotyping and copLAB PCR, we demonstrated that the genetic structure of the copper-resistant strains from these three regions was made up of two distant clusters and varied for the detection of copLAB amplicons...
January 19, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28100651/stabilization-of-bacillus-circulans-xylanase-by-combinatorial-insertional-fusion-to-a-thermophilic-host-protein
#2
Vandan Shah, Brennal Pierre, Tamari Kirtadze, Seung Shin, Jin Ryoun Kim
High thermostability of an enzyme is critical for its industrial application. While many engineering approaches such as mutagenesis have enhanced enzyme thermostability, they often suffer from reduced enzymatic activity. A thermally stabilized enzyme with unchanged amino acids is preferable for subsequent functional evolution necessary to address other important industrial needs. In the research presented here, we applied insertional fusion to a thermophilic maltodextrin-binding protein from Pyrococcus furiosus (PfMBP) in order to improve the thermal stability of Bacillus circulans xylanase (BCX)...
January 17, 2017: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/28100305/environment-directed-activation-the-escherichia-coli-flhdc-operon-by-transposons
#3
Zhongge Zhang, Chika Kukita, Mir Zafri Humayun, Milton H Saier
The flagellar system in E. coli K12 is expressed under the control of the flhDC-encoded master regulator, FlhDC. Transposition of insertion sequence (IS) elements to the upstream flhDC promoter region up-regulates transcription of this operon, resulting in more rapid motility. Wang and Wood (2011) provided evidence that insertion of IS5 into upstream activating sites occurs at higher rates in semisolid agar media in which swarming behavior is allowed as compared with liquid or solid media where swarming cannot occur...
January 17, 2017: Microbiology
https://www.readbyqxmd.com/read/28097405/role-of-exopolysaccharide-in-salt-stress-resistance-and-cell-motility-of-mesorhizobium-alhagi-ccnwxj12-2-t
#4
Xiaodong Liu, Yantao Luo, Zhefei Li, Jiamei Wang, Gehong Wei
Mesorhizobium alhagi, a legume-symbiont soil bacterium that forms nodules with the desert plant Alhagi sparsifolia, can produce large amounts of exopolysaccharide (EPS) using mannitol as carbon source. However, the role of EPS in M. alhagi CCNWXJ12-2(T), an EPS-producing rhizobium with high salt resistance, remains uncharacterized. Here, we studied the role of EPS in M. alhagi CCNWXJ12-2(T) using EPS-deficient mutants constructed by transposon mutagenesis. The insertion sites of six EPS-deficient mutants were analyzed using single primer PCR, and two putative gene clusters were found to be involved in EPS synthesis...
January 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28096490/comprehensive-essentiality-analysis-of-the-mycobacterium-tuberculosis-genome-via-saturating-transposon-mutagenesis
#5
Michael A DeJesus, Elias R Gerrick, Weizhen Xu, Sae Woong Park, Jarukit E Long, Cara C Boutte, Eric J Rubin, Dirk Schnappinger, Sabine Ehrt, Sarah M Fortune, Christopher M Sassetti, Thomas R Ioerger
: For decades, identifying the regions of a bacterial chromosome that are necessary for viability has relied on mapping integration sites in libraries of random transposon mutants to find loci that are unable to sustain insertion. To date, these studies have analyzed subsaturated libraries, necessitating the application of statistical methods to estimate the likelihood that a gap in transposon coverage is the result of biological selection and not the stochasticity of insertion. As a result, the essentiality of many genomic features, particularly small ones, could not be reliably assessed...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096365/unlocking-tn3-family-transposase-activity-in-vitro-unveils-an-asymetric-pathway-for-transposome-assembly
#6
Emilien Nicolas, Cédric A Oger, Nathan Nguyen, Michaël Lambin, Amandine Draime, Sébastien C Leterme, Michael Chandler, Bernard F J Hallet
The Tn3 family is a widespread group of replicative transposons that are notorious for their contribution to the dissemination of antibiotic resistance and the emergence of multiresistant pathogens worldwide. The TnpA transposase of these elements catalyzes DNA breakage and rejoining reactions required for transposition. It also is responsible for target immunity, a phenomenon that prevents multiple insertions of the transposon into the same genomic region. However, the molecular mechanisms whereby TnpA acts in both processes remain unknown...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096347/human-transposon-insertion-profiling-analysis-visualization-and-identification-of-somatic-line-1-insertions-in-ovarian-cancer
#7
Zuojian Tang, Jared P Steranka, Sisi Ma, Mark Grivainis, Nemanja Rodić, Cheng Ran Lisa Huang, Ie-Ming Shih, Tian-Li Wang, Jef D Boeke, David Fenyö, Kathleen H Burns
Mammalian genomes are replete with interspersed repeats reflecting the activity of transposable elements. These mobile DNAs are self-propagating, and their continued transposition is a source of both heritable structural variation as well as somatic mutation in human genomes. Tailored approaches to map these sequences are useful to identify insertion alleles. Here, we describe in detail a strategy to amplify and sequence long interspersed element-1 (LINE-1, L1) retrotransposon insertions selectively in the human genome, transposon insertion profiling by next-generation sequencing (TIPseq)...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28087716/the-piggybac-transposon-derived-genes-tpb1-and-tpb6-mediate-essential-transposon-like-excision-during-the-developmental-rearrangement-of-key-genes-in-tetrahymena-thermophila
#8
Chao-Yin Cheng, Janet M Young, Chih-Yi Gabriela Lin, Ju-Lan Chao, Harmit S Malik, Meng-Chao Yao
Ciliated protozoans perform extreme forms of programmed somatic DNA rearrangement during development. The model ciliate Tetrahymena thermophila removes 34% of its germline micronuclear genome from somatic macronuclei by excising thousands of internal eliminated sequences (IESs), a process that shares features with transposon excision. Indeed, piggyBac transposon-derived genes are necessary for genome-wide IES excision in both Tetrahymena (TPB2 [Tetrahymena piggyBac-like 2] and LIA5) and Paramecium tetraurelia (PiggyMac)...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28081459/targeted-delivery-of-in-situ-pcr-amplified-sleeping-beauty-transposon-genes-to-cancer-cells-with-lipid-based-nanoparticle-like-protocells
#9
Kun Ma, Duo Fu, Dongli Yu, Changhao Cui, Li Wang, Zhaoming Guo, Chuanbin Mao
A Sleeping Beauty (SB) transposon system is made of a transposon plasmid (containing gene encoding a desired functional or therapeutic protein) and a transposase plasmid (encoding an enzyme capable of cutting and pasting the gene into the host cell genome). It is a kind of natural, nonviral gene delivery vehicle, which can achieve efficient genomic insertion, providing long-term transgenic expression. However, before the SB transposon system could play a role in promoting gene expression, it has to be delivered efficiently first across cell membrane and then into cell nuclei...
January 2, 2017: Biomaterials
https://www.readbyqxmd.com/read/28079877/genome-wide-transposon-screening-and-quantitative-insertion-site-sequencing-for-cancer-gene-discovery-in-mice
#10
Mathias J Friedrich, Lena Rad, Iraad F Bronner, Alexander Strong, Wei Wang, Julia Weber, Matthew Mayho, Hannes Ponstingl, Thomas Engleitner, Carolyn Grove, Anja Pfaus, Dieter Saur, Juan Cadiñanos, Michael A Quail, George S Vassiliou, Pentao Liu, Allan Bradley, Roland Rad
Transposon-mediated forward genetics screening in mice has emerged as a powerful tool for cancer gene discovery. It pinpoints cancer drivers that are difficult to find with other approaches, thus complementing the sequencing-based census of human cancer genes. We describe here a large series of mouse lines for insertional mutagenesis that are compatible with two transposon systems, PiggyBac and Sleeping Beauty, and give guidance on the use of different engineered transposon variants for constitutive or tissue-specific cancer gene discovery screening...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28073968/variants-of-abgri3-carrying-the-arma-gene-in-extensively-antibiotic-resistant-acinetobacter-baumannii-from-singapore
#11
Grace A Blackwell, Kathryn E Holt, Stephen D Bentley, Li Yang Hsu, Ruth M Hall
OBJECTIVES: To investigate the context of the ribosomal RNA methyltransferase gene armA in carbapenem-resistant global clone 2 (GC2) Acinetobacter baumannii isolates from Singapore. METHODS: Antibiotic resistance was determined using disc diffusion; PCR was used to identify resistance genes. Whole genome sequences were determined and contigs were assembled and ordered using PCR. Resistance regions in unsequenced isolates were mapped. RESULTS: Fifteen GC2 A...
January 10, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28073961/genetic-characterization-of-mcr-1-bearing-plasmids-to-depict-molecular-mechanisms-underlying-dissemination-of-the-colistin-resistance-determinant
#12
Ruichao Li, Miaomiao Xie, Jinfei Zhang, Zhiqiang Yang, Lizhang Liu, Xiaobo Liu, Zhiwei Zheng, Edward Wai-Chi Chan, Sheng Chen
OBJECTIVES: To analyse and compare mcr-1-bearing plasmids from animal Escherichia coli isolates, and to investigate potential mechanisms underlying dissemination of mcr-1. METHODS: Ninety-seven ESBL-producing E. coli strains isolated from pig farms in China were screened for the mcr-1 gene. Fifteen mcr-1-positive strains were subjected to molecular characterization and bioinformatic analysis of the mcr-1-bearing plasmids that they harboured. RESULTS: Three major types of mcr-1-bearing plasmids were recovered: IncX4 (∼33 kb), IncI2 (∼60 kb) and IncHI2 (∼216-280 kb), among which the IncX4 and IncI2 plasmids were found to harbour the mcr-1 gene only, whereas multiple resistance elements including blaCTX-M, blaCMY, blaTEM, fosA, qnrS, floR and oqxAB were detected, in various combinations, alongside mcr-1 in the IncHI2 plasmids...
September 28, 2016: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28072891/molecular-epidemiology-and-resistome-analysis-of-multidrug-resistant-st11-klebsiella-pneumoniae-strain-containing-multiple-copies-of-extended-spectrum-%C3%AE-lactamase-genes-using-whole-genome-sequencing
#13
Roshan DSouza, Naina Adren Pinto, Insik Hwang, Hwang Younjee, YoungLag Cho, Hyunsoo Kim, Dongeun Yong, Jongrak Choi, Kyungwon Lee, Yunsop Chong
The aim of this work was to investigate the mechanism responsible for multidrug resistance in ST11 Klebsiella pneumoniae YMC 2013/7/B3993 containing multiple copies of ESBL genes using multiple parallel sequencing technology. In-depth analysis of the strain revealed multiple copies of ESBL genes, 2 copies of blaSHV-12 and 1 copy of blaCTX-M-15. Furthermore, 1 copy of blaOXA-9 and 3 copies of blaTEM-1 were found. The insertion of Tn1331 was detected, which consisted of blaOXA-9, blaTEM-1, aac(6')-lb-cr, and aadA1 genes...
January 10, 2017: New Microbiologica
https://www.readbyqxmd.com/read/28069706/dna-sequence-properties-that-predict-susceptibility-to-epiallelic-switching
#14
Marco Catoni, Jayne Griffiths, Claude Becker, Nicolae Radu Zabet, Carlos Bayon, Mélanie Dapp, Michal Lieberman-Lazarovich, Detlef Weigel, Jerzy Paszkowski
Transgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genomewide DNA methylation in partial and complete loss-of-function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability, which allowed us to classify chromosomal targets of epigenetic regulation into (i) single copy and methylated exclusively at CpGs, readily forming epialleles, and (ii) transposon-derived, methylated at all cytosines, which may or may not form epialleles...
January 9, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28068217/manual-curation-and-reannotation-of-the-genomes-of-clostridium-difficile-630%C3%AE-erm-and-clostridium-difficile-630
#15
Henning Dannheim, Thomas Riedel, Meina Neumann-Schaal, Boyke Bunk, Isabel Schober, Cathrin Spröer, Cynthia Maria Chibani, Sabine Gronow, Heiko Liesegang, Jörg Overmann, Dietmar Schomburg
We resequenced the genome of Clostridium difficile 630Δerm (DSM 28645), a model strain commonly used for the generation of insertion mutants. The genome sequence was obtained by a combination of single-molecule real-time (SMRT) and Illumina sequencing technology. Detailed manual curation and comparison to the previously published genomic sequence revealed sequence differences including inverted regions and the presence of plasmid pCD630. Manual curation of our previously deposited genome sequence of the parental strain 630 (DSM 27543) led to an improved genome sequence...
January 9, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28065891/genetic-and-biochemical-characterization-of-hmb-1-a-novel-subclass-b1-metallo-%C3%AE-lactamase-found-in-a-pseudomonas-aeruginosa-clinical-isolate
#16
Niels Pfennigwerth, Felix Lange, Cristina Belmar Campos, Moritz Hentschke, Sören G Gatermann, Martin Kaase
OBJECTIVES: To characterize a novel subclass B1 metallo-β-lactamase (MBL) found in an MDR Pseudomonas aeruginosa clinical isolate. METHODS: The isolate P. aeruginosa NRZ-03096 was recovered in 2012 from an anal swab from a patient hospitalized in Northern Germany and showed high MICs of carbapenems. MBL production was analysed by several phenotypic tests. Genetic characterization of the novel bla gene and MLST was performed by WGS. The novel bla gene was expressed in Escherichia coli TOP10 and the enzyme was subjected to biochemical characterization to determine the kinetic parameters Km and kcat RESULTS: P...
January 8, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28062688/piggybac-mediates-efficient-in-vivo-crispr-library-screening-for-tumorigenesis-in-mice
#17
Chunlong Xu, Xiaolan Qi, Xuguang Du, Huiying Zou, Fei Gao, Tao Feng, Hengxing Lu, Shenglan Li, Xiaomeng An, Lijun Zhang, Yuanyuan Wu, Ying Liu, Ning Li, Mario R Capecchi, Sen Wu
CRISPR/Cas9 is becoming an increasingly important tool to functionally annotate genomes. However, because genome-wide CRISPR libraries are mostly constructed in lentiviral vectors, in vivo applications are severely limited as a result of difficulties in delivery. Here, we examined the piggyBac (PB) transposon as an alternative vehicle to deliver a guide RNA (gRNA) library for in vivo screening. Although tumor induction has previously been achieved in mice by targeting cancer genes with the CRISPR/Cas9 system, in vivo genome-scale screening has not been reported...
January 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28062460/large-scale-transposition-mutagenesis-of-streptomyces-coelicolor-identifies-hundreds-of-genes-influencing-antibiotic-biosynthesis
#18
Zhong Xu, Yemin Wang, Keith F Chater, Hong-Yu Ou, H Howard Xu, Zixin Deng, Meifeng Tao
: Gram-positive Streptomyces bacteria produce thousands of bioactive secondary metabolites including antibiotics. To systematically investigate genes affecting secondary metabolism, we developed a hyperactive transposase-based Tn5 transposition system and employed it to mutagenize the model species Streptomyces coelicolor, leading to the identification of 51,443 transposition insertions. These insertions were distributed randomly along the chromosome except for some preferred regions associated with relatively low GC content in the chromosomal core...
January 6, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28062003/identification-of-genes-involved-in-mycoplasma-gallisepticum-biofilm-formation-using-mini-tn4001-sgm-transposon-mutagenesis
#19
Yang Wang, Li Yi, Fanqing Zhang, Xusheng Qiu, Lei Tan, Shengqing Yu, Xiangchao Cheng, Chan Ding
Mycoplasma gallisepticum (MG) is an important pathogen that can cause chronic respiratory disease in chickens and infectious sinusitis in turkeys. MG has the ability to form biofilms. The molecular mechanisms underlying MG biofilm formation are complex and poorly understood. To better understand the mechanisms involved in biofilm formation, mini-Tn4001-SGM, a novel transposon vector containing the gentamicin gene was constructed and electroporated into MG strain Rlow. Of the 738 mutants obtained, 12 had significantly reduced capacity to form biofilms in a polystyrene microtiter-plate biofilm assay...
January 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28058687/the-reasons-of-trithorax-like-expression-disturbance-in-trl-3609-allele-of-drosophila-melanogaster
#20
D A Karagodin, N V Battulina, T I Merkulova, E M Baricheva
The regulatory region of the Trl gene was analyzed using the mutation Trl (3609) , resulting from the insertion of the P-element into the promoter region of the gene as well as mutations obtained on its basis. It is shown that two last transcription start sites, which are most often used in vitro in S2 cells, are almost not used in vivo. Experimental data indicate that transcription terminators in transposons play an important role in the decrease in the transcription level of the recipient gene.
November 2016: Doklady. Biochemistry and Biophysics
keyword
keyword
65654
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"