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https://www.readbyqxmd.com/read/29679645/sequencing-of-pt5282-ctxm-p13190-kpc-and-p30860-nr-and-comparative-genomics-analysis-of-incx8-plasmids
#1
Haihong Fang, Jiao Feng, Yuanhong Xu, Ying Zhang, Zhe Zhan, Zhe Yin, Xiongbo Duan, Bo Gao, Yigang Tong, Jinglin Wang, Yanping Luo, Erhei Dai, Dongsheng Zhou
This study proposed a replicon-based scheme for typing IncX into nine separately clustering subgroups, including IncX1α, IncX1β and IncX2-8. The complete nucleotide sequences of three IncX8 plasmids, namely pT5282-CTXM and p30860-NR from Enterobacter cloacae and p13190-KPC from Klebsiella pneumoniae, were determined and compared with all the other two previously sequenced IncX8 plasmids pCAV1043-58 and pCAV1741-16. These five plasmids possessed conserved IncX8 backbones with limited genetic variations with respect to gene content and organization, and each of them carried one or three accessory modules that harbored resistance markers and metabolic gene clusters as well as transposons, insertion sequence (IS)-based transposition units and miniature inverted repeat transposable elements, indicating that the relatively small IncX8 backbones were able to integrate various foreign genetic contents...
April 18, 2018: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29678924/sirnas-and-pirnas-collaborate-for-transposon-control-in-the-two-spotted-spider-mite
#2
Mosharrof Mondal, Kody Mansfield, Alex Flynt
RNAi has revolutionized genetic research, and is being commercialized as an insect pest control technology. Mechanisms exploited for this purpose are antiviral and therefore rapidly evolving. Ideally, RNAi will also be used for non-insect pests, however, differences in RNAi biology makes this uncertain. Tetranychus urticae (two-spotted spider mite) is a destructive non-insect pest, which has a proclivity to develop pesticide resistance. Here we provide a comprehensive study of the endogenous RNAi pathways of spider mites to inform design of exogenous RNAi triggers...
April 20, 2018: RNA
https://www.readbyqxmd.com/read/29678883/ribosome-maturation-by-the-endoribonuclease-ybey-stabilises-a-type-iii-secretion-system-transcript-required-for-virulence-of-enterohemorrhagic-escherichia-coli
#3
Sean P McAteer, Brandon M Sy, Julia L Wong, David Tollervey, David L Gally, Jai J Tree
Enterohemorrhagic Escherichia coli (EHEC) is a significant human pathogen that colonizes humans and its reservoir host, cattle. Colonization requires the expression of a type III secretion (T3S) system that injects a cocktail of effector proteins into host cells, to promote bacterial attachment and disease progression. The T3S system is tightly regulated by a complex network of transcriptional and post-transcriptional regulators. Using transposon mutagenesis, here we identified the ybeZYX-int operon as being required for normal T3S levels...
April 20, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29675009/genomic-structural-variations-affecting-virulence-during-clonal-expansion-of-pseudomonas-syringae-pv-actinidiae-biovar-3-in-europe
#4
Giuseppe Firrao, Emanuela Torelli, Cesare Polano, Patrizia Ferrante, Francesca Ferrini, Marta Martini, Simone Marcelletti, Marco Scortichini, Paolo Ermacora
Pseudomonas syringae pv. actinidiae (Psa) biovar 3 caused pandemic bacterial canker of Actinidia chinensis and Actinidia deliciosa since 2008. In Europe, the disease spread rapidly in the kiwifruit cultivation areas from a single introduction. In this study, we investigated the genomic diversity of Psa biovar 3 strains during the primary clonal expansion in Europe using single molecule real-time (SMRT), Illumina and Sanger sequencing technologies. We recorded evidences of frequent mobilization and loss of transposon Tn6212, large chromosome inversions, and ectopic integration of IS sequences (remarkably ISPsy31, ISPsy36, and ISPsy37)...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29673315/inter-genome-comparison-of-the-quorn-fungus-fusarium-venenatum-and-the-closely-related-plant-infecting-pathogen-fusarium-graminearum
#5
Robert King, Neil Andrew Brown, Martin Urban, Kim E Hammond-Kosack
BACKGROUND: The soil dwelling saprotrophic non-pathogenic fungus Fusarium venenatum, routinely used in the commercial fermentation industry, is phylogenetically closely related to the globally important cereal and non-cereal infecting pathogen F. graminearum. This study aimed to sequence, assemble and annotate the F. venenatum (strain A3/5) genome, and compare this genome with F. graminearum. RESULTS: Using shotgun sequencing, a 38,660,329 bp F. venenatum genome was assembled into four chromosomes, and a 78,618 bp mitochondrial genome...
April 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29672704/homologous-recombination-and-transposon-propagation-shape-the-population-structure-of-an-organism-from-the-deep-subsurface-with-minimal-metabolism
#6
Alexander J Probst, Jillian F Banfield
DPANN archaea are primarily known based on genomes from metagenomes and single cells. We reconstructed a complete population genome for Candidatus "Forterrea," a Diapherotrite with a predicted symbiotic lifestyle probably centered around nucleotide metabolism and RuBisCO. Genome-wide analysis of sequence variation provided insights into the processes that shape its population structure in the deep subsurface. The genome contains many transposons, yet reconstruction of a complete genome from a short-read insert data set was possible because most occurred only in some individuals...
April 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29672509/robustness-encoded-across-essential-and-accessory-replicons-of-the-ecologically-versatile-bacterium-sinorhizobium-meliloti
#7
George C diCenzo, Alex B Benedict, Marco Fondi, Graham C Walker, Turlough M Finan, Alessio Mengoni, Joel S Griffitts
Bacterial genome evolution is characterized by gains, losses, and rearrangements of functional genetic segments. The extent to which large-scale genomic alterations influence genotype-phenotype relationships has not been investigated in a high-throughput manner. In the symbiotic soil bacterium Sinorhizobium meliloti, the genome is composed of a chromosome and two large extrachromosomal replicons (pSymA and pSymB, which together constitute 45% of the genome). Massively parallel transposon insertion sequencing (Tn-seq) was employed to evaluate the contributions of chromosomal genes to growth fitness in both the presence and absence of these extrachromosomal replicons...
April 19, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29671722/the-complete-replicons-of-16-ensifer-meliloti-strains-offer-insights-into-intra-and-inter-replicon-gene-transfer-transposon-associated-loci-and-repeat-elements
#8
Matthew Nelson, Joseph Guhlin, Brendan Epstein, Peter Tiffin, Michael J Sadowsky
Ensifer meliloti (formerly Rhizobium meliloti and Sinorhizobium meliloti) is a model bacterium for understanding legume-rhizobial symbioses. The tripartite genome of E. meliloti consists of a chromosome, pSymA and pSymB, and in some instances strain-specific accessory plasmids. The majority of previous sequencing studies have relied on the use of assemblies generated from short read sequencing, which leads to gaps and assembly errors. Here we used PacBio-based, long-read assemblies and were able to assemble, de novo, complete circular replicons...
April 19, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29669108/genomic-context-of-resistance-genes-within-a-french-clinical-mdr-proteus-mirabilis-identification-of-the-novel-genomic-resistance-island-gipmi1
#9
Eliane Siebor, Claire de Curraize, Catherine Neuwirth
Objectives: To determine the location of the antibiotic resistance genes in the MDR Proteus mirabilis PmPHI clinical isolate. Methods: WGS and de novo assembly were performed. BLAST searches were used to identify relevant contigs. PCR and Sanger sequencing were used to link the fragments of interest and fill the gaps. Results: P. mirabilis PmPHI was resistant to six classes of antibiotics: penicillins, aminoglycosides, phenicols, tetracyclines, folate inhibitors and fluoroquinolones...
April 12, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29669107/dambe7-new-and-improved-tools-for-data-analysis-in-molecular-biology-and-evolution
#10
Xuhua Xia
DAMBE is a comprehensive software package for genomic and phylogenetic data analysis on Windows, Linux and Macintosh computers. New functions include imputing missing distances and phylogeny simultaneously (paving the way to build large phage and transposon trees), new bootstrapping/jackknifing methods for PhyPA (phylogenetics from pairwise alignments), and an improved function for fast and accurate estimation of the shape parameter of the gamma distribution for fitting rate heterogeneity over sites. Previous method corrects multiple hits for each site independently...
April 14, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29668013/drosophila-relics-hobo-and-hobo-mites-transposons-as-raw-material-for-new-regulatory-networks
#11
Elgion L S Loreto, Maríndia Deprá, José F Diesel, Yanina Panzera, Vera Lucia S Valente-Gaiesky
Hypermutable strains of Drosophila simulans have been studied for 20 years. Several mutants were isolated and characterized, some of which had phenotypes associated with alteration in development; for example, showing ectopic legs with eyes being expressed in place of antennae. The causal agent of this hypermutability is a non-autonomous hobo-related sequence (hoboVA). Around 100 mobilizable copies of this element are present in the D. simulans genome, and these are likely mobilized by the autonomous and canonical hobo element...
2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29667553/car-t-cell-therapy-a-new-era-in-cancer-immunotherapy
#12
Miliotou N Androulla, Papadopoulou C Lefkothea
BACKGROUND: Cancer is one of the leading causes of death worldwide. Over the years, a number of conventional cytotoxic approaches for neoplastic diseases has been developed. However, due to their limited effectiveness in accordance with the heterogeneity of cancer cells, there is a constant search for therapeutic approaches with improved outcome, such as immunotherapy that utilizes and enhances the normal capacity of the patient's immune system. METHODS: Chimeric Antigen Receptor (CAR) T-cell therapy involves genetic modification of patient's autologous T-cells to express a CAR specific for a tumor antigen, following by ex vivo cell expansion and re-infusion back to the patient...
April 17, 2018: Current Pharmaceutical Biotechnology
https://www.readbyqxmd.com/read/29666196/whole-genome-sequence-of-an-edible-and-potential-medicinal-fungus-cordyceps-guangdongensis
#13
Chenghua Zhang, Wangqiu Deng, Wenjuan Yan, Taihui Li
Cordyceps guangdongensis is an edible fungus which was approved as a novel food by the Chinese Ministry of Public Health in 2013. It also has a broad prospect of application in pharmaceutical industries, with many medicinal activities. In this study, the whole genome of C. guangdongensis GD15, a single spore isolate from a wild strain, was sequenced and assembled with Illumina and PacBio sequencing technology. The generated genome is 29.05 Mb in size, comprising nine scaffolds with an average GC content of 57...
April 17, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29663096/plasmids-carrying-dha-1-%C3%AE-lactamases
#14
REVIEW
Claire Hennequin, Viviane Ravet, Frédéric Robin
The aim of this review is to provide an update on the plasmids mediating DHA-1 cephalosporinase in Klebsiella pneumoniae. These plasmids have been mainly found in this bacterium but not only. The first was isolated from Salmonella sp. in France in the early 1990s. They are currently reported worldwide. BlaDHA-1 beta-lactamase gene is usually co-expressed with many other antibiotic resistance genes such as extended-spectrum β-lactamases (blaCTX-M -, bla SHV -types), oxacillinases (blaOXA-1, blaOXA-30 ), penicillinases (bla TEM -type), carbapenemases (bla OXA48 , blaKPC-2 ), aminoglycosides (aacA, aadA, armA), fluoroquinolones (qnrB4, aac6'-1b-cr), and sulfonamide (sul1) resistance genes...
April 17, 2018: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29662477/new-genes-involved-in-mild-stress-response-identified-by-transposon-mutagenesis-in-lactobacillus-paracasei
#15
Aurore Palud, Hélène Scornec, Jean-François Cavin, Hélène Licandro
Lactic acid bacteria (LAB) are associated with various plant, animal, and human niches and are also present in many fermented foods and beverages. Thus, they are subjected to several stress conditions and have developed advanced response mechanisms to resist, adapt, and grow. This work aimed to identify the genes involved in some stress adaptation mechanisms in LAB. For this purpose, global reverse genetics was applied by screening a library of 1287 Lactobacillus paracasei transposon mutants for mild monofactorial stresses...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29662210/genome-wide-mutant-profiling-predicts-the-mechanism-of-a-lipid-ii-binding-antibiotic
#16
Marina Santiago, Wonsik Lee, Antoine Abou Fayad, Kathryn A Coe, Mithila Rajagopal, Truc Do, Fabienne Hennessen, Veerasak Srisuknimit, Rolf Müller, Timothy C Meredith, Suzanne Walker
Identifying targets of antibacterial compounds remains a challenging step in the development of antibiotics. We have developed a two-pronged functional genomics approach to predict mechanism of action that uses mutant fitness data from antibiotic-treated transposon libraries containing both upregulation and inactivation mutants. We treated a Staphylococcus aureus transposon library containing 690,000 unique insertions with 32 antibiotics. Upregulation signatures identified from directional biases in insertions revealed known molecular targets and resistance mechanisms for the majority of these...
April 16, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29660854/the-butanol-producing-microbe-clostridium-beijerinckii-ncimb-14988-manipulated-using-forward-and-reverse-genetic-tools
#17
Gareth T Little, Benjamin J Willson, John T Heap, Klaus Winzer, Nigel P Minton
The solventogenic anaerobe Clostridium beijerinckii has potential for use in the sustainable bioconversion of plant-derived carbohydrates into solvents, such as butanol or acetone. However, relatively few strains have been extensively characterised either at the genomic level or through exemplification of a complete genetic toolkit. To remedy this situation, a new strain of C. beijerinckii, NCIMB 14988, was selected from amongst a total of 55 new clostridial isolates capable of growth on hexose and pentose sugars...
April 16, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29659873/two-new-salmonella-genomic-islands-1-from-proteus-mirabilis-and-description-of-blactx-m-15-on-a-variant-sgi1-k7
#18
Claire de Curraize, Catherine Neuwirth, Julien Bador, Angélique Chapuis, Lucie Amoureux, Eliane Siebor
Objectives: To characterize the structure of Salmonella genomic islands 1 (SGI1s) from two clinical Proteus mirabilis isolates: one producing an ESBL and the other a penicillinase. Methods: WGS completed by PCR and Sanger sequencing was performed to determine sequences of SGI1s from Pm2CHAMA and Pm37THOMI strains. Results: Two new variants of SGI1 named SGI1-Pm2CHAMA (53.6 kb) and SGI1-K7 (55.1 kb) were identified. The backbone of SGI1-Pm2CHAMA shared 99...
April 11, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29659815/plant-lineage-specific-amplification-of-transcription-factor-binding-motifs-by-miniature-inverted-repeat-transposable-elements-mites
#19
Jordi Morata, Fatima Marín, Jordi Payet, Josep M Casacuberta
Transposable elements are one of the main drivers of plant genome evolution. Transposon insertions can modify the gene coding capacity or the regulation of their expression, the latter being a more subtle effect, and therefore particularly useful for evolution. Transposons have been show to contain transcription factor binding sites that can be mobilized upon transposition with the potential to integrate new genes into transcriptional networks. MITEs are a type of non-coding DNA transposons that could be particularly suited as a vector to mobilize transcription factor binding sites and modify transcriptional networks during evolution...
April 5, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29657968/inferring-the-minimal-genome-of-mesoplasma-florum-by-comparative-genomics-and-transposon-mutagenesis
#20
Vincent Baby, Jean-Christophe Lachance, Jules Gagnon, Jean-François Lucier, Dominick Matteau, Tom Knight, Sébastien Rodrigue
The creation and comparison of minimal genomes will help better define the most fundamental mechanisms supporting life. Mesoplasma florum is a near-minimal, fast-growing, nonpathogenic bacterium potentially amenable to genome reduction efforts. In a comparative genomic study of 13 M. florum strains, including 11 newly sequenced genomes, we have identified the core genome and open pangenome of this species. Our results show that all of the strains have approximately 80% of their gene content in common. Of the remaining 20%, 17% of the genes were found in multiple strains and 3% were unique to any given strain...
May 2018: MSystems
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