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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/28057894/validating-genome-wide-association-candidates-through-quantitative-variation-in-nodulation
#14
Shaun J Curtin, Peter Tiffin, Joseph Guhlin, Diana I Trujillo, Liana T Burghardt, Paul Atkins, Nicholas J Baltes, Roxanne Denny, Daniel F Voytas, Robert M Stupar, Nevin Dale Young
Genome wide association (GWA) studies offer the opportunity to identify genes that contribute to naturally occurring variation in quantitative traits. However, GWA relies exclusively on statistical association, so functional validation is necessary to make strong claims about gene function. We used a combination of gene-disruption platforms (Tnt1 retro-transposons, hairpin RNA-interference constructs, and CRISPR/Cas9 nucleases) together with randomized, well-replicated experiments to evaluate the function of genes that an earlier GWAS in Medicago truncatula had identified as candidates contributing to variation in the symbiosis between legumes and rhizobia...
January 5, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28057802/cfs1p-a-novel-membrane-protein-in-the-pq-loop-family-is-involved-in-phospholipid-flippase-functions-in-yeast
#15
Takaharu Yamamoto, Konomi Fujimura-Kamada, Eno Shioji, Risa Suzuki, Kazuma Tanaka
Type 4 P-type ATPases (P4-ATPases) function as phospholipid flippases, which translocate phospholipids from the exoplasmic leaflet to the cytoplasmic leaflet of the lipid bilayer, to generate and maintain asymmetric distribution of phospholipids at the plasma membrane and endosomal/Golgi membranes. The budding yeast Saccharomyces cerevisiae has four heteromeric flippases (Drs2p, Dnf1p, Dnf2p, and Dnf3p), associated with the Cdc50p family noncatalytic subunit, and one monomeric flippase, Neo1p They have been suggested to function in vesicle formation in membrane trafficking pathways, but details of their mechanisms remain to be clarified...
January 5, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28057730/insertion-polymorphisms-of-mobile-genetic-elements-in-sexual-and-asexual-populations-of-daphnia-pulex
#16
Xiaoqian Jiang, Haixu Tang, Zhiqiang Ye, Michael Lynch
Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 20 sexual and 20 asexual isolates of D. pulex across North American from their available whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D...
January 4, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28053272/trans-generational-function-of-tetrahymena-piwi-protein-twi8p-at-distinctive-non-coding-rna-loci
#17
Brian M Farley, Kathleen Collins
Trans-generational transmission of genome-regulatory epigenetic information can determine phenotypes in the progeny of sexual reproduction. Sequence specificity of trans-generational regulation derives from small RNAs assembled into Piwi-protein complexes. Known targets of trans-generational regulation are primarily transposons and transposon-derived sequences. Here, we extend the scope of Piwi-mediated trans-generational regulation to include unique non-coding RNA loci. Ciliates such as Tetrahymena have a phenotypically silent germline micronucleus and an expressed somatic macronucleus, which is differentiated anew from a germline genome copy in sexual reproduction...
January 4, 2017: RNA
https://www.readbyqxmd.com/read/28052753/chromosomal-position-effect-influences-the-heterologous-expression-of-genes-and-biosynthetic-gene-clusters-in-streptomyces-albus-j1074
#18
Bohdan Bilyk, Liliya Horbal, Andriy Luzhetskyy
BACKGROUND: Efforts to construct the Streptomyces host strain with enhanced yields of heterologous product have focussed mostly on engineering of primary metabolism and/or the deletion of endogenous biosynthetic gene clusters. However, other factors, such as chromosome compactization, have been shown to have a significant influence on gene expression levels in bacteria and fungi. The expression of genes and biosynthetic gene clusters may vary significantly depending on their location within the chromosome...
January 4, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28049432/identification-of-genes-affecting-alginate-biosynthesis-in-pseudomonas-fluorescens-by-screening-a-transposon-insertion-library
#19
Helga Ertesvåg, Håvard Sletta, Mona Senneset, Yi-Qian Sun, Geir Klinkenberg, Therese Aursand Konradsen, Trond E Ellingsen, Svein Valla
BACKGROUND: Polysaccharides often are necessary components of bacterial biofilms and capsules. Production of these biopolymers constitutes a drain on key components in the central carbon metabolism, but so far little is known concerning if and how the cells divide their resources between cell growth and production of exopolysaccharides. Alginate is an industrially important linear polysaccharide synthesized from fructose 6-phosphate by several bacterial species. The aim of this study was to identify genes that are necessary for obtaining a normal level of alginate production in alginate-producing Pseudomonas fluorescens...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28046014/pseudomonas-aeruginosa-sera-gene-is-required-for-bacterial-translocation-through-caco-2-cell-monolayers
#20
Masashi Yasuda, Syouya Nagata, Satoshi Yamane, Chinami Kunikata, Yutaka Kida, Koichi Kuwano, Chigusa Suezawa, Jun Okuda
To specify critical factors responsible for Pseudomonas aeruginosa penetration through the Caco-2 cell epithelial barrier, we analyzed transposon insertion mutants that demonstrated a dramatic reduction in penetration activity relative to P. aeruginosa PAO1 strain. From these strains, mutations could be grouped into five classes, specifically flagellin-associated genes, pili-associated genes, heat-shock protein genes, genes related to the glycolytic pathway, and biosynthesis-related genes. Of these mutants, we here focused on the serA mutant, as the association between this gene and penetration activity is yet unknown...
2017: PloS One
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