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https://www.readbyqxmd.com/read/28231340/the-widely-used-nicotiana-benthamiana-16c-line-has-an-unusual-t-dna-integration-pattern-including-a-transposon-sequence
#1
Joshua G Philips, Fatima Naim, Michał T Lorenc, Kevin J Dudley, Roger P Hellens, Peter M Waterhouse
Nicotiana benthamiana is employed around the world for many types of research and one transgenic line has been used more extensively than any other. This line, 16c, expresses the Aequorea victoria green fluorescent protein (GFP), highly and constitutively, and has been a major resource for visualising the mobility and actions of small RNAs. Insights into the mechanisms studied at a molecular level in N. benthamiana 16c are likely to be deeper and more accurate with a greater knowledge of the GFP gene integration site...
2017: PloS One
https://www.readbyqxmd.com/read/28229965/atmbd6-a-methyl-cpg-binding-domain-protein-maintains-gene-silencing-in-arabidopsis-by-interacting-with-rna-binding-proteins
#2
Adwaita Prasad Parida, Amrapali Sharma, Arun Kumar Sharma
DNA methylation, mediated by double-stranded RNA, is a conserved epigenetic phenomenon that protects a genome from transposons, silences unwanted genes and has a paramount function in plant or animal development. Methyl CpG binding domain proteins are members of a class of proteins that bind to methylated DNA. The Arabidopsis thaliana genome encodes 13 methyl CpG binding domain (MBD) proteins, but the molecular/biological functions of most of these proteins are still not clear. In the present study, we identified four proteins that interact with AtMBD6...
March 2017: Journal of Biosciences
https://www.readbyqxmd.com/read/28228545/ablation-of-rnai-and-retrotransposons-accompany-acquisition-and-evolution-of-transposases-to-heterochromatin-protein-cenpb
#3
Udita Upadhyay, Suchita Srivastava, Indu Khatri, Jagpreet Singh Nanda, Srikrishna Subramanian, Amit Arora, Jagmohan Singh
Inactivation of retrotransposons is accompanied by the emergence of CENPB (centromere binding protein-B) in Schizosaccharomyces as well as in metazoans. The RNAi-induced Transcriptional Silencing (RITS) Complex, comprising Chp1 (chromodomain protein-1), Tas3 (protein with unknown function) and Ago1 (Argonaute), plays an important role in RNAi-mediated heterochromatinization. We find that while the Ago1 subunit of the RITS complex is highly conserved, Tas3 is lost and Chp1 is truncated in S. cryophilus and S...
February 22, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28228480/a-stable-but-reversible-integrated-surrogate-reporter-for-assaying-crispr-cas9-stimulated-homology-directed-repair
#4
Yahong Wen, Grace Liao, Thomas Pritchard, Ting-Ting Zhao, Jon P Connelly, Shondra M Pruett-Miller, Valerie Blanc, Nicholas O Davidson, Blair B Madison
The discovery and application of CRISPR/Cas9 technology for genome editing has greatly accelerated targeted mutagenesis in a variety of organisms. CRISPR/Cas9-mediated site-specific cleavage is typically exploited for the generation of insertions or deletions (indels) following aberrant dsDNA repair via the endogenous non-homology end-joining (NHEJ) pathway, or alternatively, for enhancing homology directed repair (HDR) to facilitate the generation of a specific mutation (or knock-in). However, there is a need for efficient cellular assays that can measure Cas9/guide RNA (gRNA) activity...
February 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28223389/analysis-of-serial-isolates-of-mcr-1-positive-escherichia-coli-reveals-a-highly-active-isapl1-transposon
#5
Erik Snesrud, Ana C Ong, Brendan Corey, Yoon I Kwak, Robert Clifford, Todd Gleeson, Shannon Wood, Timothy J Whitman, Emil P Lesho, Mary Hinkle, Patrick Mc Gann
The emergence of the transferable colistin resistance gene mcr-1 is of global concern. The insertion sequence (IS) Apl1 is a key component in the mobilization of this gene, but its role remains poorly understood.Six Escherichia coli were cultured from the same patient over one month in Germany and the USA after a brief hospitalization in Bahrain for an unconnected illness. Four carried mcr-1 by real-time PCR, but two were negative. Two additional mcr-1-negative E. coli were collected during follow-up surveillance nine months later...
February 21, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28221375/circadian-deep-sequencing-reveals-stress-response-genes-that-adopt-robust-rhythmic-expression-during-aging
#6
Rachael C Kuintzle, Eileen S Chow, Tara N Westby, Barbara O Gvakharia, Jadwiga M Giebultowicz, David A Hendrix
Disruption of the circadian clock, which directs rhythmic expression of numerous output genes, accelerates aging. To enquire how the circadian system protects aging organisms, here we compare circadian transcriptomes in heads of young and old Drosophila melanogaster. The core clock and most output genes remained robustly rhythmic in old flies, while others lost rhythmicity with age, resulting in constitutive over- or under-expression. Unexpectedly, we identify a subset of genes that adopted increased or de novo rhythmicity during aging, enriched for stress-response functions...
February 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28220152/lack-of-mycothiol-and-ergothioneine-induces-different-protective-mechanisms-in-mycobacterium-smegmatis
#7
Arishma Rajkarnikar Singh, Andrew Strankman, Ruzan Orkusyan, Endang Purwantini, Mamta Rawat
Mycobacterium smegmatis contains the low molecular weight thiols, mycothiol (MSH) and ergothioneine (ESH). Examination of transposon mutants disrupted in mshC and egtA, involved in the biosynthesis of MSH and ESH respectively, demonstrated that both mutants were sensitive to oxidative, alkylating, and metal stress. However, the mshC mutant exhibited significantly more protein carbonylation and lipid peroxidation than wildtype, while the egtA mutant had less protein and lipid damage than wildtype. We further show that Ohr, KatN, and AhpC, involved in protection against oxidative stress, are upregulated in the egtA mutant...
December 2016: Biochemistry and Biophysics Reports
https://www.readbyqxmd.com/read/28220115/spread-of-the-blaoxa-23-containing-tn2008-in-carbapenem-resistant-acinetobacter-baumannii-isolates-grouped-in-cc92-from-china
#8
Yisheng Chen, Jing Gao, Haomin Zhang, Chunmei Ying
The rapid expansion of carbapenem-resistant Acinetobacter baumannii (CRAB) clinical isolates is a big issue. We investigated the antibiotic susceptibility, molecular epidemiology and resistance gene of A. baumannii collected at two hospitals in Shanghai, China. Besides, the A. baumannii PCR-based replicon typing method (AB-PBRT) was conducted to categorize the plasmids into homogeneous groups on the basis of replicase genes. Most CRAB isolates showed high-level resistance to almost all antibiotics but retain susceptibility to colistin and tigecycline...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28219662/fumarase-deficiency-causes-protein-and-metabolite-succination-and-intoxicates-mycobacterium-tuberculosis
#9
Nadine Ruecker, Robert Jansen, Carolina Trujillo, Susan Puckett, Pradeepa Jayachandran, Gerardo G Piroli, Norma Frizzell, Henrik Molina, Kyu Y Rhee, Sabine Ehrt
Enzymes of central carbon metabolism are essential mediators of Mycobacterium tuberculosis (Mtb) physiology and pathogenicity, but are often perceived to lack sufficient species selectivity to be pursued as potential drug targets. Fumarase (Fum) is an enzyme of the canonical tricarboxylic acid cycle and is dispensable in many organisms. Transposon mutagenesis studies in Mtb, however, indicate that Fum is required for optimal growth. Here, we report the generation and characterization of a genetically engineered Mtb strain in which Fum expression is conditionally regulated...
February 9, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28212410/a-high-throughput-genetic-screen-identifies-previously-uncharacterized-borrelia-burgdorferi-genes-important-for-resistance-against-reactive-oxygen-and-nitrogen-species
#10
Meghan E Ramsey, Jenny A Hyde, Diana N Medina-Perez, Tao Lin, Lihui Gao, Maureen E Lundt, Xin Li, Steven J Norris, Jon T Skare, Linden T Hu
Borrelia burgdorferi, the causative agent of Lyme disease in humans, is exposed to reactive oxygen and nitrogen species (ROS and RNS) in both the tick vector and vertebrate reservoir hosts. B. burgdorferi contains a limited repertoire of canonical oxidative stress response genes, suggesting that novel gene functions may be important for protection of B. burgdorferi against ROS or RNS exposure. Here, we use transposon insertion sequencing (Tn-seq) to conduct an unbiased search for genes involved in resistance to nitric oxide, hydrogen peroxide, and tertiary-butyl hydroperoxide in vitro...
February 17, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28207953/sgs1-a-neomorphic-nac52-allele-impairing-ptgs-through-sgs3-down-regulation
#11
Nicolas Butel, Ivan Le Masson, Nathalie Bouteiller, Hervé Vaucheret, Taline Elmayan
Post-transcriptional gene silencing (PTGS) is a defense mechanism that targets invading nucleic acids from endogenous (transposons) or exogenous (pathogens, transgenes) origins. Genetic screens based on the reactivation of silenced transgenes have long been used to identify cellular PTGS components and regulators. Here we show that the first isolated PTGS-deficient mutant, sgs1, is impaired in the transcription factor NAC52. This mutant exhibits striking similarities with a mutant impaired in the H3K4me3 demethylase JMJ14 isolated from the same genetic screen...
February 16, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28207789/carbapenem-resistance-and-pathogenicity-of-bovine-acinetobacter-indicus-like-isolates
#12
Peter Klotz, Stephan Göttig, Ursula Leidner, Torsten Semmler, Sandra Scheufen, Christa Ewers
The objective of this study was to characterize blaOXA-23 harbouring Acinetobacter indicus-like strains from cattle including genomic and phylogenetic analyses, antimicrobial susceptibility testing and evaluation of pathogenicity in vitro and in vivo. Nasal and rectal swabs (n = 45) from cattle in Germany were screened for carbapenem-non-susceptible Acinetobacter spp. Thereby, two carbapenem resistant Acinetobacter spp. from the nasal cavities of two calves could be isolated. MALDI-TOF mass spectrometry and 16S rDNA sequencing identified these isolates as A...
2017: PloS One
https://www.readbyqxmd.com/read/28204924/genome-wide-analysis-of-transposable-elements-in-the-coffee-berry-borer-hypothenemus-hampei-coleoptera-curculionidae-description-of-novel-families
#13
Eric M Hernandez-Hernandez, Rita Daniela Fernández-Medina, Lucio Navarro-Escalante, Jonathan Nuñez, Pablo Benavides-Machado, Claudia M A Carareto
The coffee berry borer (CBB) Hypothenemus hampei is the most limiting pest of coffee production worldwide. The CBB genome has been recently sequenced; however, information regarding the presence and characteristics of transposable elements (TEs) was not provided. Using systematic searching strategies based on both de novo and homology-based approaches, we present a library of TEs from the draft genome of CBB sequenced by the Colombian Coffee Growers Federation. The library consists of 880 sequences classified as 66% Class I (LTRs: 46%, non-LTRs: 20%) and 34% Class II (DNA transposons: 8%, Helitrons: 16% and MITEs: 10%) elements, including families of the three main LTR (Gypsy, Bel-Pao and Copia) and non-LTR (CR1, Daphne, I/Nimb, Jockey, Kiri, R1, R2 and R4) clades and DNA superfamilies (Tc1-mariner, hAT, Merlin, P, PIF-Harbinger, PiggyBac and Helitron)...
February 15, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28199335/ecological-networks-to-unravel-the-routes-to-horizontal-transposon-transfers
#14
Samuel Venner, Vincent Miele, Christophe Terzian, Christian Biémont, Vincent Daubin, Cédric Feschotte, Dominique Pontier
Transposable elements (TEs) represent the single largest component of numerous eukaryotic genomes, and their activity and dispersal constitute an important force fostering evolutionary innovation. The horizontal transfer of TEs (HTT) between eukaryotic species is a common and widespread phenomenon that has had a profound impact on TE dynamics and, consequently, on the evolutionary trajectory of many species' lineages. However, the mechanisms promoting HTT remain largely unknown. In this article, we argue that network theory combined with functional ecology provides a robust conceptual framework and tools to delineate how complex interactions between diverse organisms may act in synergy to promote HTTs...
February 2017: PLoS Biology
https://www.readbyqxmd.com/read/28199212/transposon-mediated-directed-mutation-in-bacteria-and-eukaryotes
#15
Milton H Saier, Chika Kukita, Zhongge Zhang
Transposon-mediated "directed" mutations occur at higher frequencies when beneficial than when detrimental and relieve the stress that causes them. The first and best-studied example involves regulation of Insertion Sequence-5 (IS5) insertion into a specific activating site upstream of the glycerol utilization operon in Escherichia coli, glpFK. This event promotes high level expression of the glpFK operon, allowing glycerol utilization in wild type cells under inhibitory conditions. The phosphoenolpyruvate-dependent, sugar transporting, phosphotransferase system (PTS) influences this process by regulating cytoplasmic glycerol-3-phosphate and cyclic AMP concentrations...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28198411/the-secondary-resistome-of-multidrug-resistant-klebsiella-pneumoniae
#16
Bimal Jana, Amy K Cain, William T Doerrler, Christine J Boinett, Maria C Fookes, Julian Parkhill, Luca Guardabassi
Klebsiella pneumoniae causes severe lung and bloodstream infections that are difficult to treat due to multidrug resistance. We hypothesized that antimicrobial resistance can be reversed by targeting chromosomal non-essential genes that are not responsible for acquired resistance but essential for resistant bacteria under therapeutic concentrations of antimicrobials. Conditional essentiality of individual genes to antimicrobial resistance was evaluated in an epidemic multidrug-resistant clone of K. pneumoniae (ST258)...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28193840/co-chaperone-hsp70-hsp90-organizing-protein-hop-is-required-for-transposon-silencing-and-pirna-biogenesis
#17
Joseph A Karam, Rasesh Y Parikh, Dhananjaya Nayak, David Rosenkranz, Vamsi K Gangaraju
piRNAs are 26-30nt germ-line specific small non-coding RNAs that have evolutionarily conserved function in mobile genetic element (transposons) silencing and maintenance of genome integrity. Drosophila Hsp70/90 Organizing Protein Homolog (Hop), a co-chaperone, interacts with piRNA binding protein Piwi and mediates silencing of phenotypic variations. However, it is not known if Hop has a direct role in piRNA biogenesis and transposon silencing. Here, we show that knockdown of Hop in the germ-line nurse cells (GLKD) of Drosophila ovaries leads to activation of transposons...
February 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28193652/characterization-of-the-plasmid-pjb12-from-pseudomonas-aeruginosa-reveals-tn6352-a-novel-putative-transposon-associated-with-mobilization-of-blavim-2-harboring-in58-integron
#18
João Botelho, Filipa Grosso, Luísa Peixe
blaVIM-2-carrying In58 integron has been linked to a chromosomal location in different bacterial species, including Pseudomonas aeruginosa This work reports the first fully sequenced In58-harboring plasmid, significantly different from the two previously identified blaVIM-2-carrying plasmids in P. aeruginosablaVIM-2 was possibly acquired by transposition of Tn6352, a novel transposon composed by In58 and ISPa17 element. The recognition of similar IR sites by ISPa17 demonstrates a common mobilization process associated with blaVIM-2 and blaVIM-1 genes acquisition...
February 13, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28188692/bioreactor-scale-up-and-protein-product-quality-characterization-of-piggybac-transposon-derived-cho-pools
#19
Yashas Rajendra, Sowmya Balasubramanian, Robert B Peery, James R Swartling, Neil A McCracken, Dawn L Norris, Christopher C Frye, Gavin C Barnard
Chinese hamster ovary (CHO) cells remain the most popular host for the production of biopharmaceutical drugs, particularly monoclonal antibodies (mAbs), bispecific antibodies and Fc-fusion proteins. Creating and characterizing the stable CHO clonally-derived cell lines (CDCLs) needed to manufacture these therapeutic proteins is a lengthy and laborious process. Therefore, CHO pools have increasingly been used to rapidly produce protein to support and enable preclinical drug development. We recently described the generation of CHO pools yielding mAb titers as high as 7...
February 11, 2017: Biotechnology Progress
https://www.readbyqxmd.com/read/28188204/siderophore-product-ornibactin-is-required-for-the-bactericidal-activity-of-burkholderia-contaminans-ms14
#20
Peng Deng, Adam Foxfire, Jianhong Xu, Sonya M Baird, Jiayuan Jia, Keren H Delgado, Ronald Shin, Leif Smith, Shi-En Lu
Burkholderia contaminans MS14 was isolated from soil in Mississippi. When cultivated on nutrient broth-yeast extract (NBY) agar medium, the colonies exhibit bactericidal activity against a wide range of plant pathogenic bacteria. Only a bacteriostatic compound with siderophore activity was successfully purified, which was determined by nuclear magnetic resonance (NMR) to be ornibactin. The isolation of the bactericidal compound has not yet been achieved, thus, the exact nature of the bactericidal compound is still unknown...
February 10, 2017: Applied and Environmental Microbiology
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