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https://www.readbyqxmd.com/read/29046683/the-diversity-of-sequence-and-chromosomal-distribution-of-new-transposable-element-related-segments-in-the-rye-genome-revealed-by-fish-and-lineage-annotation
#1
Yingxin Zhang, Chengming Fan, Shuangshuang Li, Yuhong Chen, Richard R-C Wang, Xiangqi Zhang, Fangpu Han, Zanmin Hu
Transposable elements (TEs) in plant genomes exhibit a great variety of structure, sequence content and copy number, making them important drivers for species diversity and genome evolution. Even though a genome-wide statistic summary of TEs in rye has been obtained using high-throughput DNA sequencing technology, the accurate diversity of TEs in rye, as well as their chromosomal distribution and evolution, remains elusive due to the repetitive sequence assembling problems and the high dynamic and nested nature of TEs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29046400/ribosome-biogenesis-modulates-ty1-copy-number-control-in-saccharomyces-cerevisiae
#2
Hyo Won Ahn, Jessica M Tucker, Joshua A Arribere, David J Garfinkel
Transposons can impact the host genome by altering gene expression and participating in chromosome rearrangements. Therefore, organisms evolved different ways to minimize the level of transposition. In Saccharomyces cerevisiae and its close relative S. paradoxus, Ty1 copy number control (CNC) is mediated by the self-encoded restriction factor p22, which is derived from the GAG capsid gene and inhibits virus-like particle (VLP) assembly and function. Based on secondary screens of Ty1 cofactors, we identified LOC1, a RNA localization/ribosome biogenesis gene that affects Ty1 mobility predominantly in strains harboring Ty1 elements...
October 18, 2017: Genetics
https://www.readbyqxmd.com/read/29044738/overview-of-mechanisms-of-antibiotic-resistance-in-pseudomonas-aeruginosa-an-ocular-perspective
#3
REVIEW
Dinesh Subedi, Ajay Kumar Vijay, Mark Willcox
Treatment of Pseudomonas aeruginosa eye infections often becomes a challenge due to the ability of this bacterium to be resistant to antibiotics via intrinsic and acquired mechanisms. Transfer of resistance due to interchangeable genetic elements is an important mechanism for the rapid transfer of antibiotic resistance in this pathogen. As a result, drug-resistant strains are becoming increasingly prevalent worldwide. This review systematically analyses data from recent publications to describe the global prevalence and antibiotic sensitivity of ocular P...
October 18, 2017: Clinical & Experimental Optometry: Journal of the Australian Optometrical Association
https://www.readbyqxmd.com/read/29043376/enhanced-rhamnolipid-production-in-burkholderia-thailandensis-transposon-knockout-strains-deficient-in-polyhydroxyalkanoate-pha-synthesis
#4
Scott J Funston, Konstantina Tsaousi, Thomas J Smyth, Matthew S Twigg, Roger Marchant, Ibrahim M Banat
Microbially produced rhamnolipids have significant commercial potential; however, the main bacterial producer, Pseudomonas aeruginosa, is an opportunistic human pathogen, which limits biotechnological exploitation. The non-pathogenic species Burkholderia thailandensis produces rhamnolipids; however, yield is relatively low. The aim of this study was to determine whether rhamnolipid production could be increased in Burkholderia thailandensis through mutation of genes responsible for the synthesis of the storage material polyhydroxyalkanoate (PHA), thereby increasing cellular resources for the production of rhamnolipids...
October 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29038910/analysis-of-somaclonal-variation-in-transgenic-and-regenerated-plants-of-arabidopsis-thaliana-using-methylation-related-metaflp-and-tmd-markers
#5
Carlos J Coronel, Ana I González, María L Ruiz, Carlos Polanco
We provide evidence that nucleotide sequence and methylation status changes occur in the Arabidopsis genome during in vitro tissue culture at a frequency high enough to represent an important source of variation. Somaclonal variation is a general consequence of the tissue culture process that has to be analyzed specifically when regenerated plants are obtained in any plant species. Currently, there are few studies about the variability comprising sequence changes and methylation status at the DNA level, generated by the culture of A...
October 16, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29036477/a-single-active-site-in-the-mariner-transposase-cleaves-dna-strands-of-opposite-polarity
#6
Corentin Claeys Bouuaert, Ronald Chalmers
The RNase H structural fold defines a large family of nucleic acid metabolizing enzymes that catalyze phosphoryl transfer reactions using two divalent metal ions in the active site. Almost all of these reactions involve only one strand of the nucleic acid substrates. In contrast, cut-and-paste transposases cleave two DNA strands of opposite polarity, which is usually achieved via an elegant hairpin mechanism. In the mariner transposons, the hairpin intermediate is absent and key aspects of the mechanism by which the transposon ends are cleaved remained unknown...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036456/role-of-free-dna-ends-and-protospacer-adjacent-motifs-for-crispr-dna-uptake-in-pyrococcus-furiosus
#7
Masami Shiimori, Sandra C Garrett, Dwain P Chambers, Claiborne V C Glover, Brenton R Graveley, Michael P Terns
To acquire CRISPR-Cas immunity against invasive mobile genetic elements, prokaryotes must first integrate fragments of foreign DNA into their genomic CRISPR arrays for use in future invader silencing. Here, we found that the hyperthermophilic archaeaon, Pyrococcus furiosus, actively incorporates DNA fragments (spacers) from both plasmid (foreign) and host genome (self) sequences into its seven CRISPR loci. The majority of new spacers were derived from DNA immediately downstream from a 5'-CCN-3' protospacer adjacent motif (PAM) that is critical for invader targeting...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29032658/analysis-of-protein-expression-in-brucella-abortus-mutants-with-different-growth-rates-by-two-dimensional-gel-electrophoresis-and-lc-ms-ms-peptide-analysis
#8
Woo Bin Park, Young Bin Im, Shim Soojin, Han Sang Yoo
Brucella abortus is a bacterium that causes brucellosis and is the causative agent of worldwide zoonosis. Pathogenesis of the Brucella abortus infection is so complicates. Thus, several researches have made to solve mechanism in infection of Brucella abortus. While several proteins are revealed as the pathogenic factors by previous researches, underlying mechanism of the Brucella abortus infection is still left to be resolved. We identify the proteins showing the different expression level in Brucella abortus mutants with different biological characteristics that generated by random insertion of transposon...
October 13, 2017: Journal of Veterinary Science
https://www.readbyqxmd.com/read/29032547/genome-wide-mutagenesis-in-borrelia-burgdorferi
#9
Tao Lin, Lihui Gao
Signature-tagged mutagenesis (STM) is a functional genomics approach to identify bacterial virulence determinants and virulence factors by simultaneously screening multiple mutants in a single host animal, and has been utilized extensively for the study of bacterial pathogenesis, host-pathogen interactions, and spirochete and tick biology. The signature-tagged transposon mutagenesis has been developed to investigate virulence determinants and pathogenesis of Borrelia burgdorferi. Mutants in genes important in virulence are identified by negative selection in which the mutants fail to colonize or disseminate in the animal host and tick vector...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29032444/modulating-signaling-networks-by-crispr-cas9-mediated-transposable-element-insertion
#10
REVIEW
Luis María Vaschetto
In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it...
October 14, 2017: Current Genetics
https://www.readbyqxmd.com/read/29030443/a-novel-metabolic-pathway-for-n-methylpyrrolidone-degradation-in-alicycliphilus-sp-bq1
#11
Claudia Julieta Solís-González, Lilianha Domínguez-Malfavón, Martín Vargas-Suárez, Itzel Gaytán, Miguel Ángel Cevallos, Luis Lozano, M Javier Cruz-Gómez, Herminia Loza-Tavera
The molecular mechanisms underlying the biodegradation of N-Methylpyrrolidone (NMP), a widely used industrial solvent that produces skin irritation in humans, and is teratogenic in rats, are unknown. Alicycliphilus sp. BQ1 degrades NMP. By studying a transposon-tagged mutant unable to degrade NMP, we identified a six-gene cluster (nmpABCDEF), transcribed as a polycistronic mRNA, encoding enzymes involved in NMP biodegradation. nmpA and the transposon-affected gene nmpB encode a N-methylhydantoin amidohydrolase that would transform NMP to γ-N-methylaminobutyric acid; this would be metabolized by an aminoacid oxidase (NMPC), either by demethylation to produce γ-aminobutyric acid (GABA), or by deamination to produce succinate semialdehyde (SSA)...
October 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29029114/carbapenem-resistant-citrobacter-spp-isolated-in-spain-from-2013-to-2015-produced-a-variety-of-carbapenemases-including-vim-1-oxa-48-kpc-2-ndm-1-and-vim-2
#12
David M Arana, Adriana Ortega, Eva González-Barberá, Noelia Lara, Verónica Bautista, Dolores Gómez-Ruíz, David Sáez, Sara Fernández-Romero, Belén Aracil, María Pérez-Vázquez, José Campos, Jesús Oteo
Objectives: There is little information about carbapenemase-producing (CP) Citrobacter spp. We studied the molecular epidemiology and microbiological features of CP Citrobacter spp. isolates collected in Spain (2013-15). Methods: In total, 119 isolates suspected of being CP by the EUCAST screening cut-off values were analysed. Carbapenemases and ESBLs were characterized using PCR and sequencing. The genetic relationship among Citrobacter freundii isolates was studied by PFGE...
September 27, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29029084/penicillin-binding-protein-encoded-by-pbp4-is-involved-in-mediating-copper-stress-in-listeria-monocytogenes
#13
Cameron Parsons, Ben Costolo, Phillip Brown, Sophia Kathariou
Listeria monocytogenes raises major food safety and public health concerns due its potential for severe foodborne disease and persistent colonization of food processing facilities. Copper is often employed to control pathogens in agriculture and is increasingly used in healthcare facilities, but mechanisms mediating tolerance of L. monocytogenes to copper remain poorly understood. A mariner-based mutant library of L. monocytogenes 2011L-2858, implicated in the 2011 listeriosis outbreak via whole cantaloupe, was screened for growth at sublethal levels of copper yielding mutant G2B4 with decreased copper tolerance...
October 4, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29027482/structural-genomics-of-pndm-btr-harboring-in191-and-tn6360-and-other-bla-ndm-carrying-incn1-plasmids
#14
Yachao Zhao, Lijun Wang, Zhiyi Zhang, Jiao Feng, Huaixing Kang, Liqun Fang, Xiaoyuan Jiang, Defu Zhang, Zhe Zhan, Dongsheng Zhou, Yigang Tong
AIM: To characterize a conjugative bla NDM-1-carrying plasmid pNDM-BTR from a clinical Escherichia coli isolate. MATERIALS & METHODS: The complete nucleotide sequence of pNDM-BTR was determined using next-generation sequencing technology. Comparative genomic analysis of bla NDM-carrying IncN1 plasmids, including pNDM-BTR, was performed, and the antimicrobial resistance phenotypes were determined. RESULTS: pNDM-BTR contained three accessory modules, namely IS26, a novel Tn3-family transposon Tn6360 and the dfrA14 region composed of In191, ecoRII-ecoRIImet and ΔIS1X2...
October 13, 2017: Future Microbiology
https://www.readbyqxmd.com/read/29026163/revealing-the-saline-adaptation-strategies-of-the-halophilic-bacterium-halomonas-beimenensis-through-high-throughput-omics-and-transposon-mutagenesis-approaches
#15
Yan-Huey Chen, Chia-Wei Lu, Yuan-Tay Shyu, Shih-Shun Lin
Studies on the halotolerance of bacteria are attractive to the fermentation industry. However, a lack of sufficient genomic information has precluded an investigation of the halotolerance of Halomonas beimenensis. Here, we describe the molecular mechanisms of saline adaptation in H. beimenensis based on high-throughput omics and Tn5 transposon mutagenesis. The H. beimenensis genome is 4.05 Mbp and contains 3,807 genes, which were sequenced using short and long reads obtained via deep sequencing. Sixteen Tn5 mutants with a loss of halotolerance were identified...
October 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29026162/improving-membrane-protein-expression-and-function-using-genomic-edits
#16
Heather M Jensen, Thomas Eng, Victor Chubukov, Robin A Herbert, Aindrila Mukhopadhyay
Expression of membrane proteins often leads to growth inhibition and perturbs central metabolism and this burden varies with the protein being overexpressed. There are also known strain backgrounds that allow greater expression of membrane proteins but that differ in efficacy across proteins. We hypothesized that for any membrane protein, it may be possible to identify a modified strain background where its expression can be accommodated with less burden. To directly test this hypothesis, we used a bar-coded transposon insertion library in tandem with cell sorting to assess genome-wide impact of gene deletions on membrane protein expression...
October 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29025411/maize-rna-poliv-affects-the-expression-of-genes-with-nearby-te-insertions-and-has-a-genome-wide-repressive-impact-on-transcription
#17
Cristian Forestan, Silvia Farinati, Riccardo Aiese Cigliano, Alice Lunardon, Walter Sanseverino, Serena Varotto
BACKGROUND: RNA-directed DNA methylation (RdDM) is a plant-specific epigenetic process that relies on the RNA polymerase IV (Pol IV) for the production of 24 nucleotide small interfering RNAs (siRNA) that guide the cytosine methylation and silencing of genes and transposons. Zea mays RPD1/RMR6 gene encodes the largest subunit of Pol IV and is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs) and transcriptional regulation of specific alleles...
October 12, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29022867/response-to-photo-oxidative-stress-of-pseudomonas-aeruginosa-pao1-mutants-impaired-in-different-functions
#18
Viviana Teresa Orlandi, Fabrizio Bolognese, Eleonora Martegani, Vincenzo Cantaluppi, Claudio Medana, Paola Barbieri
Clinicians often have to deal with infections that are difficult to control because they are caused by superbugs resistant to many antibiotics. Alternatives to antibiotic treatment include antimicrobial photodynamic therapy (aPDT). The photodynamic process causes bacterial death, inducing oxidative stress through the photoactivation of photosensitizer molecules in the presence of oxygen. No PDT-resistant bacteria have been selected to date, thus the response to photo-oxidative stress in non-phototrophic bacteria needs further investigation...
October 12, 2017: Microbiology
https://www.readbyqxmd.com/read/29018935/a-curious-new-role-for-mrn-in-schizosaccharomyces-pombe-non-homologous-end-joining
#19
REVIEW
Kurt W Runge, Yanhui Li
Chromosomal breaks can be healed by several repair processes, including one called non-homologous end-joining (NHEJ) where the two broken ends are ligated together with a loss of 0-5 bp of DNA. The protein requirements for NHEJ of cut DNA ends in the budding yeast Saccharomyces cerevisiae include its version of the Mre11-Rad50-Nbs1 (MRN) complex. In contrast, the fission yeast Schizosaccharomyces pombe and mammalian cells do not require MRN for this process. Recent work in S. pombe used transposon excision to generate breaks that were capped by DNA hairpins, which must be opened to produce ligatable ends...
October 10, 2017: Current Genetics
https://www.readbyqxmd.com/read/29018421/himar1-transposon-for-efficient-random-mutagenesis-in-aggregatibacter-actinomycetemcomitans
#20
Qinfeng Ding, Kai Soo Tan
Aggregatibacter actinomycetemcomitans is the primary etiological agent of aggressive periodontal disease. Identification of novel virulence factors at the genome-wide level is hindered by lack of efficient genetic tools to perform mutagenesis in this organism. The Himar1 mariner transposon is known to yield a random distribution of insertions in an organism's genome with requirement for only a TA dinucleotide target and is independent of host-specific factors. However, the utility of this system in A. actinomycetemcomitans is unknown...
2017: Frontiers in Microbiology
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