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https://www.readbyqxmd.com/read/28212378/sequencing-the-extrachromosomal-circular-mobilome-reveals-retrotransposon-activity-in-plants
#1
Sophie Lanciano, Marie-Christine Carpentier, Christel Llauro, Edouard Jobet, Dagmara Robakowska-Hyzorek, Eric Lasserre, Alain Ghesquière, Olivier Panaud, Marie Mirouze
Retrotransposons are mobile genetic elements abundant in plant and animal genomes. While efficiently silenced by the epigenetic machinery, they can be reactivated upon stress or during development. Their level of transcription not reflecting their transposition ability, it is thus difficult to evaluate their contribution to the active mobilome. Here we applied a simple methodology based on the high throughput sequencing of extrachromosomal circular DNA (eccDNA) forms of active retrotransposons to characterize the repertoire of mobile retrotransposons in plants...
February 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28205536/genomic-structure-and-insertion-sites-of-helicobacter-pylori-prophages-from-various-geographical-origins
#2
Filipa F Vale, Alexandra Nunes, Mónica Oleastro, João P Gomes, Daniel A Sampaio, Raquel Rocha, Jorge M B Vítor, Lars Engstrand, Ben Pascoe, Elvire Berthenet, Samuel K Sheppard, Matthew D Hitchings, Francis Mégraud, Jamuna Vadivelu, Philippe Lehours
Helicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The genome sizes of these prophages range from 22.6-33.0 Kbp, consisting of 27-39 open reading frames...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28194158/role-and-regulation-of-acc-deaminase-gene-in-sinorhizobium-meliloti-is-it-a-symbiotic-rhizospheric-or-endophytic-gene
#3
Alice Checcucci, Elisa Azzarello, Marco Bazzicalupo, Anna De Carlo, Giovanni Emiliani, Stefano Mancuso, Giulia Spini, Carlo Viti, Alessio Mengoni
Plant-associated bacteria exhibit a number of different strategies and specific genes allow bacteria to communicate and metabolically interact with plant tissues. Among the genes found in the genomes of plant-associated bacteria, the gene encoding the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) is one of the most diffused. This gene is supposed to be involved in the cleaving of plant-produced ACC, the precursor of the plant stress-hormone ethylene toning down the plant response to infection...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28193905/assessment-of-insertion-sequence-mobilization-as-an-adaptive-response-to-oxidative-stress-in-acinetobacter-baumannii-using-is-seq
#4
Meredith S Wright, Stephanie Mountain, Karen Beeri, Mark D Adams
Insertion sequence (IS) elements are found throughout bacterial genomes and contribute to genome variation by interrupting genes or altering gene expression. Few of the more than thirty IS elements described in Acinetobacter baumannii have been characterized for transposition activity or expression effects. A targeted sequencing method, IS-seq, was developed to efficiently map the locations of new insertion events in A. baumannii genomes and was used to identify novel IS sites following growth in the presence of hydrogen peroxide, which causes oxidative stress...
February 13, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28193840/co-chaperone-hsp70-hsp90-organizing-protein-hop-is-required-for-transposon-silencing-and-pirna-biogenesis
#5
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/28187792/evolution-of-rna-and-dna-guided-antivirus-defense-systems-in-prokaryotes-and-eukaryotes-common-ancestry-vs-convergence
#6
REVIEW
Eugene V Koonin
: Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation...
February 10, 2017: Biology Direct
https://www.readbyqxmd.com/read/28181543/meca-related-structure-in-methicillin-resistant-coagulase-negative-staphylococci-from-street-food-in-taiwan
#7
Tsung-Ying Yang, Wei-Wen Hung, Lin Lin, Wei-Chun Hung, Sung-Pin Tseng
Antibiotic-resistant patterns, a mecA homologue complex, and staphylococcal cassette chromosome mec (SCCmec) were analysed in samples of ready-to-eat (RTE) street food in Taiwan. RTE food samples (270) were collected in three densely populated Taiwanese cities between June and November 2014. Among 14 strains being identified as methicillin-resistant coagulase-negative staphylococci (MRCoNS), genetic diversities was determined by PFGE analysis. SCCmec types IV, V, VIII and TXG-24 were detected in 9, and mecASs (a mecA homologue) detected in 8...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28179422/viruses-comprise-an-extensive-pool-of-mobile-genetic-elements-in-eukaryote-cell-cultures-and-human-clinical-samples
#8
Jakob Thannesberger, Hans-Joerg Hellinger, Ingeborg Klymiuk, Marie-Theres Kastner, Franz J J Rieder, Martina Schneider, Susanne Fister, Thomas Lion, Karin Kosulin, Johannes Laengle, Michael Bergmann, Thomas Rattei, Christoph Steininger
Viruses shape a diversity of ecosystems by modulating their microbial, eukaryotic, or plant host metabolism. The complexity of virus-host interaction networks is progressively fathomed by novel metagenomic approaches. By using a novel metagenomic method, we explored the virome in mammalian cell cultures and clinical samples to identify an extensive pool of mobile genetic elements in all of these ecosystems. Despite aseptic treatment, cell cultures harbored extensive and diverse phage populations with a high abundance of as yet unknown and uncharacterized viruses (viral dark matter)...
February 8, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28174306/a-mobile-element-in-muts-drives-hypermutation-in-a-marine-vibrio
#9
Nathaniel D Chu, Sean A Clarke, Sonia Timberlake, Martin F Polz, Alan D Grossman, Eric J Alm
: Bacteria face a trade-off between genetic fidelity, which reduces deleterious mistakes in the genome, and genetic innovation, which allows organisms to adapt. Evidence suggests that many bacteria balance this trade-off by modulating their mutation rates, but few mechanisms have been described for such modulation. Following experimental evolution and whole-genome resequencing of the marine bacterium Vibrio splendidus 12B01, we discovered one such mechanism, which allows this bacterium to switch to an elevated mutation rate...
February 7, 2017: MBio
https://www.readbyqxmd.com/read/28167525/the-history-of-bordetella-pertussis-genome-evolution-includes-structural-rearrangement
#10
Michael R Weigand, Yanhui Peng, Vladimir Loparev, Dhwani Batra, Katherine E Bowden, Mark Burroughs, Pamela K Cassiday, Jamie K Davis, Taccara Johnson, Phalasy Juieng, Kristen Knipe, Marsenia H Mathis, Andrea M Pruitt, Lori Rowe, Mili Sheth, M Lucia Tondella, Margaret M Williams
: Despite high pertussis vaccine coverage, reported cases of whooping cough (pertussis) have increased over the last decade in the United States and other developed countries. Although Bordetella pertussis is well known for its limited gene sequence variation, recent advances in long-read sequencing technology have begun to reveal genome structural heterogeneity among otherwise indistinguishable isolates, even within geographically or temporally defined epidemics. We have compared rearrangements among complete genome assemblies from 257 B...
February 6, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28143782/esbl-ampc-and-carbapenemase-producing-enterobacteriaceae-in-animals-a-threat-for-humans
#11
REVIEW
Jean-Yves Madec, Marisa Haenni, Patrice Nordmann, Laurent Poirel
There has been a great and long-term concern that ESBL/AmpC- and carbapenemase-producing Enterobacteriaceae occurring in animals may constitute a public health issue. A large number of factors with complex interrelations contribute to the spread of those bacteria among animals and humans. ESBL/AmpC- or carbapenemase-encoding genes are most often located onto mobile genetic elements favouring their dissemination. Some shared reservoirs of ESBL/AmpC or carbapenemase genes, plasmids or clones have been identified and suggest cross-transmissions...
January 28, 2017: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28143440/emergence-and-spread-of-a-new-community-genotype-methicillin-resistant-staphylococcus-aureus-clone-in-colombia
#12
Javier Escobar-Perez, Niradiz Reyes, Ricaurte Alejandro Marquez-Ortiz, Juan Rebollo, Hernando Pinzón, Catalina Tovar, Jaime Moreno-Castañeda, Zayda Lorena Corredor, Betsy Esperanza Castro, Maria Victoria Moncada, Natasha Vanegas
BACKGROUND: Community-genotype methicillin-resistant Staphylococcus aureus (CG-MRSA) clones are a global concern due to their resistance and increased virulence and their ability to cause infections both hospitalized patients and healthy people in the community. Here, we characterize 32 isolates of a new CG-MRSA clone. These isolates were identified in four cities in Colombia, South America. METHODS: The isolates were recovered from four different epidemiological and prospective studies that were conducted in several regions of Colombia...
January 31, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28138100/transposase-mediated-excision-conjugative-transfer-and-diversity-of-ice6013-in-staphylococcus-aureus
#13
Emily A Sansevere, Xiao Luo, Joo Youn Park, Sunghyun Yoon, Keun Seok Seo, D Ashley Robinson
: ICE6013 represents one of two families of integrative conjugative elements (ICEs) identified in the pan-genome of the human and animal pathogen, Staphylococcus aureus Here we investigate the excision and conjugation functions of ICE6013 and further characterize the diversity of this element. ICE6013 excision is not significantly affected by growth, temperature, pH or UV exposure and does not depend on recA The IS30-like DDE transposase (Tpase; orf1 and orf2) of ICE6013 must be uninterrupted for excision to occur, whereas disruption of three other orfs on the element significantly affect the level of excision...
January 30, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28137804/a-clostridium-difficile-lineage-endemic-to-costa-rican-hospitals-is-multidrug-resistant-by-acquisition-of-chromosomal-mutations-and-novel-mobile-genetic-elements
#14
Gabriel Ramírez-Vargas, Carlos Quesada-Gómez, Luis Acuña-Amador, Diana López-Ureña, Tatiana Murillo, María Del Mar Gamboa-Coronado, Esteban Chaves-Olarte, Nicholas Thomson, Evelyn Rodríguez-Cavallini, César Rodríguez
The antimicrobial resistance rates and levels recorded for Clostridium difficile are on the rise. This study reports the nature, levels, diversity, and genomic context of the antimicrobial resistance of human C. difficile isolates from the NAPCR1/RT012/ST54 genotype, which caused an outbreak in 2009 and is endemic in Costa Rican hospitals. To this end, we determined the susceptibility of 38 NAPCR1 isolates to ten antibiotics from seven classes using E-tests or macrodilution tests and examined 31 NAPCR1 whole-genome sequences to identify single nucleotide polymorphisms and genes that could explain the observed resistance phenotypes...
January 30, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28126386/the-occurrence-of-antibiotic-resistance-genes-in-a-mediterranean-river-and-their-persistence-in-the-riverbed-sediment
#15
William Calero-Cáceres, Javier Méndez, Julia Martín-Díaz, Maite Muniesa
The spread of antibiotic resistance genes (ARGs) in the environment is a serious concern. Bacterial ARGs can spread via different mobile genetic elements as phage particles, which thereby emerge as novel vectors for environmental dissemination. To assess how climate events, such as heavy rains or water scarcity, could affect the spread of ARGs, it is necessary to know their prevalence and abundance in aquatic environments as well as the potential reservoirs from which they could become mobile. This study evaluates the occurrence of ARGs in the water and sediment of a Mediterranean river...
January 23, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28120911/a-potential-role-of-transposon-is431-in-the-loss-of-meca-gene
#16
Aihua Wang, Kai Zhou, Yang Liu, Liang Yang, Qin Zhang, Jing Guan, Nanshan Zhong, Chao Zhuo
Acquisition of a vancomycin-resistance-determinant may trigger deletion of the mecA gene. However, the molecular mechanisms involved remain largely unknown. In this study, we successfully produced vancomycin-intermediate-resistant Staphylococcus aureus (VISA) from Methicillin-resistant-S. aureus (MRSA) through serial passages with vancomycin. Five MRSA isolates achieved a vancomycin MIC of >8 mg/ml after 45-day serial exposure to vancomycin. After 20-day passages in media without antibiotics, three of the isolates were restored to pre-induction levels, whilst the remaining 2 (3503-1 and 4126-1) retained a vancomycin MIC >6 mg/ml...
January 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28111461/diversity-and-evolution-of-class-2-crispr-cas-systems
#17
REVIEW
Sergey Shmakov, Aaron Smargon, David Scott, David Cox, Neena Pyzocha, Winston Yan, Omar O Abudayyeh, Jonathan S Gootenberg, Kira S Makarova, Yuri I Wolf, Konstantin Severinov, Feng Zhang, Eugene V Koonin
Class 2 CRISPR-Cas systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the discovery of novel class 2 variants and used it to identify six new CRISPR-Cas subtypes. The diverse properties of these new systems provide potential for the development of versatile tools for genome editing and regulation. In this Analysis article, we present a comprehensive census of class 2 types and class 2 subtypes in complete and draft bacterial and archaeal genomes, outline evolutionary scenarios for the independent origin of different class 2 CRISPR-Cas systems from mobile genetic elements, and propose an amended classification and nomenclature of CRISPR-Cas...
January 23, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28111326/molecular-characterisations-of-integrons-in-clinical-isolates-of-klebsiella-pneumoniae-in-a-chinese-tertiary-hospital
#18
Xuan Xu, Xuan Li, Mei Luo, Pin Liu, Kewen Su, Ying Qing, Shuai Chen, Jingfu Qiu, Yingli Li
BACKGROUND: Integrons are mobile genetic elements that play an important role in the distribution of antibiotic-resistance genes among bacteria. This study aimed to investigate the distribution of integrons in clinical isolates of Klebsiella pneumoniae and explore the molecular mechanism of integron-mediated multiple-drug resistance in K. pneumoniae. METHODS: Class 1, 2, and 3 integrases were identified by polymerase chain reaction (PCR) among 178 K. pneumoniae clinical isolates...
January 20, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28107719/occurrence-and-elimination-of-antibiotic-resistance-genes-in-a-long-term-operation-integrated-surface-flow-constructed-wetland
#19
Hansun Fang, Qin Zhang, Xiangping Nie, Baowei Chen, Yuandong Xiao, Qiubai Zhou, Wei Liao, Ximei Liang
Wetland construction is a recommended domestic sewage treatment technique, owing to its simplicity and cost efficiency. Concentrations of 14 antibiotic resistance genes (ARGs) in an integrated surface flow constructed wetland (ICW) steadily operated over 10 years were investigated in the winter and summer. Domestic sewage was observed to be the primary source of ARGs in the ICW, and 77.8% and 59.5% removal rates of total targeted ARGs in the ICW were achieved in the winter and summer, respectively. Concentrations of five ARGs (sul1, tetA, tetC, tetE, and qnrS) in the winter and of six ARGs (sul1, sul3, tetA, tetC, tetE, and qnrS) in the summer were increased throughout the treatment process...
January 6, 2017: Chemosphere
https://www.readbyqxmd.com/read/28103802/proteomics-informed-by-transcriptomics-for-characterising-active-transposable-elements-and-genome-annotation-in-aedes-aegypti
#20
Kevin Maringer, Amjad Yousuf, Kate J Heesom, Jun Fan, David Lee, Ana Fernandez-Sesma, Conrad Bessant, David A Matthews, Andrew D Davidson
BACKGROUND: Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable elements (TEs). Transposons have been linked to diverse cellular processes, including the establishment of viral persistence in insects, an essential step in the transmission of vector-borne viruses. However, up until now it has not been possible to study the overall proteome derived from an organism's mobile genetic elements, partly due to the highly divergent nature of TEs...
January 19, 2017: BMC Genomics
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