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https://www.readbyqxmd.com/read/28538166/an-evolutionary-perspective-on-plasmid-lifestyle-modes
#1
REVIEW
Nils Hülter, Judith Ilhan, Tanita Wein, A Samer Kadibalban, Katrin Hammerschmidt, Tal Dagan
Plasmids are extra-chromosomal genetic elements whose ecology and evolution depend on their genetic repertoire and interaction with the host. We review the events that lead to transitions between plasmid lifestyle modes - invasion, host range, plasmid persistence and adaptation - from a plasmid perspective. Plasmid lifestyle is determined by various traits, including mobility, stability and indispensability that vary in their magnitude. Transitions between the plasmid lifestyles, invasion, host range, plasmid persistence and adpatation, are caused by the interplay between plasmid traits and host biology...
May 21, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28528649/metal-resistance-and-its-association-with-antibiotic-resistance
#2
Chandan Pal, Karishma Asiani, Sankalp Arya, Christopher Rensing, Dov J Stekel, D G Joakim Larsson, Jon L Hobman
Antibiotic resistance is recognised as a major global threat to public health by the World Health Organization. Currently, several hundred thousand deaths yearly can be attributed to infections with antibiotic-resistant bacteria. The major driver for the development of antibiotic resistance is considered to be the use, misuse and overuse of antibiotics in humans and animals. Nonantibiotic compounds, such as antibacterial biocides and metals, may also contribute to the promotion of antibiotic resistance through co-selection...
2017: Advances in Microbial Physiology
https://www.readbyqxmd.com/read/28528306/the-group-ii-intron-maturase-a-reverse-transcriptase-and-splicing-factor-go-hand-in-hand
#3
REVIEW
Chen Zhao, Anna Marie Pyle
The splicing of group II introns in vivo requires the assistance of a multifunctional intron encoded protein (IEP, or maturase). Each IEP is also a reverse-transcriptase enzyme that enables group II introns to behave as mobile genetic elements. During splicing or retro-transposition, each group II intron forms a tight, specific complex with its own encoded IEP, resulting in a highly reactive holoenzyme. This review focuses on the structural basis for IEP function, as revealed by recent crystal structures of an IEP reverse transcriptase domain and cryo-EM structures of an IEP-intron complex...
May 18, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28526788/zinc-resistance-within-swine-associated-methicillin-resistant-staphylococcus-aureus-mrsa-isolates-in-the-usa-is-associated-with-mlst-lineage
#4
Samantha J Hau, Timothy Frana, Jisun Sun, Peter R Davies, Tracy L Nicholson
Zinc resistance in livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) sequence type (ST) 398 is primarily mediated by the czrC gene co-located with the mecA gene, encoding methicillin resistance, within the type V SCCmec element. Because czrC and mecA are located within the same mobile genetic element, it has been suggested that the use of in feed zinc as an antidiarrheal agent has the potential to contribute to the emergence and spread of MRSA in swine through increased selection pressure to maintain the SCCmec element in isolates obtained from pigs...
May 19, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28525572/crosstalk-between-vertical-and-horizontal-gene-transfer-plasmid-replication-control-by-a-conjugative-relaxase
#5
Fabián Lorenzo-Díaz, Cris Fernández-López, Rudi Lurz, Alicia Bravo, Manuel Espinosa
Horizontal gene transfer is a key process in the evolution of bacteria and also represents a source of genetic variation in eukaryotes. Among elements participating in gene transfer, thousands of small (<10 kb) mobile bacterial plasmids that replicate by the rolling circle mechanism represent a driving force in the spread of antibiotic resistances. In general, these plasmids are built as genetic modules that encode a replicase, an antibiotic-resistance determinant, and a relaxase that participates in their conjugative mobilization...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28512627/laboratory-mice-are-frequently-colonized-with-staphylococcus-aureus-and-mount-a-systemic-immune-response-note-of-caution-for-in-vivo-infection-experiments
#6
Daniel Schulz, Dorothee Grumann, Patricia Trübe, Kathleen Pritchett-Corning, Sarah Johnson, Kevin Reppschläger, Janine Gumz, Nandakumar Sundaramoorthy, Stephan Michalik, Sabine Berg, Jens van den Brandt, Richard Fister, Stefan Monecke, Benedict Uy, Frank Schmidt, Barbara M Bröker, Siouxsie Wiles, Silva Holtfreter
Whether mice are an appropriate model for S. aureus infection and vaccination studies is a matter of debate, because they are not considered as natural hosts of S. aureus. We previously identified a mouse-adapted S. aureus strain, which caused infections in laboratory mice. This raised the question whether laboratory mice are commonly colonized with S. aureus and whether this might impact on infection experiments. Publicly available health reports from commercial vendors revealed that S. aureus colonization is rather frequent, with rates as high as 21% among specific-pathogen-free mice...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28503377/analysis-of-reca-independent-recombination-events-between-short-direct-repeats-related-to-a-genomic-island-and-to-a-plasmid-in-escherichia-coli-k12
#7
María F Azpiroz, Magela Laviña
RecA-independent recombination events between short direct repeats, leading to deletion of the intervening sequences, were found to occur in two genetic models in the Escherichia coli K12 background. The first model was a small E. coli genomic island which had been shown to be mobile in its strain of origin and, when cloned, also in the E. coli K12 context. However, it did not encode a site-specific recombinase as mobile genomic islands usually do. It was then deduced that the host cells should provide the recombination function...
2017: PeerJ
https://www.readbyqxmd.com/read/28491150/dynamic-silencing-of-somatic-l1-retrotransposon-insertions-reflects-the-developmental-and-cellular-contexts-of-their-genomic-integration
#8
Manoj Kannan, Jingfeng Li, Sarah E Fritz, Kathryn E Husarek, Jonathan C Sanford, Teresa L Sullivan, Pawan Kumar Tiwary, Wenfeng An, Jef D Boeke, David E Symer
BACKGROUND: The ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive, real-time L1 retrotransposon reporter constructs. RESULTS: Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human cancer cells, mouse embryonic stem cells, and tissues of pseudofounder transgenic mice and their progeny...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28479289/nationwide-surveillance-of-clinical-carbapenem-resistant-enterobacteriaceae-cre-strains-in-china
#9
Rong Zhang, Lizhang Liu, Hongwei Zhou, Edward Waichi Chan, Jiaping Li, Ying Fang, Yi Li, Kang Liao, Sheng Chen
The increasing incidence of carbapenem-resistant Enterobacteriaceae (CRE) - mediated hospital infections in China prompted a need to investigate the genetic basis of emergence of such strains. A nationwide survey was conducted in China covering a total of 1105 CRE strains collected from 25 geographical locales with results showing that acquisition of two carbapenemase genes, blaKPC-2 and blaNDM, was responsible for phenotypic resistance in 90% of the CRE strains tested (58% and 32% respectively), among which several major strain types, such as ST11 of K...
April 26, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28475713/tcdd-influences-reservoir-of-antibiotic-resistance-genes-in-murine-gut-microbiome
#10
Robert D Stedtfeld, Tiffany M Stedtfeld, Kelly A Fader, Maggie R Williams, Prianca Bhaduri, John Quensen, Timothy R Zacharewski, James M Tiedje, Syed A Hashsham
Dysbiosis of the gut microbiome via antibiotics, changes in diet, and infection can select for bacterial groups that more frequently harbor antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). However, the impact of environmental toxicants on the reservoir of ARGs in the gut microbiome has received less attention. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a potent aryl hydrocarbon receptor (AhR) agonist with multiple toxic health effects including immune dysfunction. The selective pressure of TCDD on the abundance of ARG and MGE harboring gut populations was examined using C57BL/6 mice exposed to 0-30 μg/kg TCDD for 28 and 92 days with the latter having a 30-day recovery period...
May 4, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28472712/casposons-mobile-genetic-elements-that-gave-rise-to-the-crispr-cas-adaptation-machinery
#11
REVIEW
Mart Krupovic, Pierre Béguin, Eugene V Koonin
A casposon, a member of a distinct superfamily of archaeal and bacterial self-synthesizing transposons that employ a recombinase (casposase) homologous to the Cas1 endonuclease, appears to have given rise to the adaptation module of CRISPR-Cas systems as well as the CRISPR repeats themselves. Comparison of the mechanistic features of the reactions catalyzed by the casposase and the Cas1-Cas2 heterohexamer, the CRISPR integrase, reveals close similarity but also important differences that explain the requirement of Cas2 for integration of short DNA fragments, the CRISPR spacers...
May 1, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28469420/in-silico-approach-for-characterization-and-comparison-of-repeats-in-the-genomes-of-oil-and-date-palms
#12
Jaire Alves Ferreira Filho, Lucas Soares de Brito, André Pereira Leão, Alexandre Alonso Alves, Eduardo Fernandes Formighieri, Manoel Teixeira Souza Júnior
Transposable elements (TEs) are mobile genetic elements present in almost all eukaryotic genomes. Due to their typical patterns of repetition, discovery, and characterization, they demand analysis by various bioinformatics software. Probably, as a result of the need for a complex analysis, many genomes publicly available do not have these elements annotated yet. In this study, a de novo and homology-based identification of TEs and microsatellites was performed using genomic data from 3 palm species: Elaeis oleifera (American oil palm, v...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28467369/developmental-control-of-nramp1-slc11a1-expression-in-professional-phagocytes
#13
Mathieu F M Cellier
NRAMP1 (SLC11A1) is a professional phagocyte membrane importer of divalent metals that contributes to iron recycling at homeostasis and to nutritional immunity against infection. Analyses of data generated by several consortia and additional studies were integrated to hypothesize mechanisms restricting NRAMP1 expression to mature phagocytes. Results from various epigenetic and transcriptomic approaches were collected for mesodermal and hematopoietic cell types and compiled for combined analysis with results of genetic studies associating single nucleotide polymorphisms (SNPs) with variations in NRAMP1 expression (eQTLs)...
May 3, 2017: Biology
https://www.readbyqxmd.com/read/28462927/de-novo-evolved-interference-competition-promotes-the-spread-of-biofilm-defectors
#14
Marivic Martin, Anna Dragoš, Theresa Hölscher, Gergely Maróti, Balázs Bálint, Martin Westermann, Ákos T Kovács
Biofilms are social entities where bacteria live in tightly packed agglomerations, surrounded by self-secreted exopolymers. Since production of exopolymers is costly and potentially exploitable by non-producers, mechanisms that prevent invasion of non-producing mutants are hypothesized. Here we study long-term dynamics and evolution in Bacillus subtilis biofilm populations consisting of wild-type (WT) matrix producers and mutant non-producers. We show that non-producers initially fail to incorporate into biofilms formed by the WT cells, resulting in 100-fold lower final frequency compared to the WT...
May 2, 2017: Nature Communications
https://www.readbyqxmd.com/read/28460328/isothermal-assay-targeting-class-1-integrase-gene-for-environmental-surveillance-of-antibiotic-resistance-markers
#15
Robert D Stedtfeld, Tiffany M Stedtfeld, Hassen Waseem, Meridith Fitschen-Brown, Xueping Guo, Benli Chai, Maggie R Williams, Trevor Shook, Amanda Logan, Ally Graham, Jong-Chan Chae, Woo-Jun Sul, Jacob VanHouten, James R Cole, Gerben J Zylstra, James M Tiedje, Brad L Upham, Syed A Hashsham
Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP)...
April 28, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28458094/in-and-out-contribution-of-natural-transformation-to-the-shuffling-of-large-genomic-regions
#16
REVIEW
Melanie Blokesch
Naturally competent bacteria can pull free DNA from their surroundings. This incoming DNA can serve various purposes, ranging from acting as a source of nutrients or DNA stretches for repair to the acquisition of novel genetic information. The latter process defines the natural competence for transformation as a mode of horizontal gene transfer (HGT) and led to its discovery almost a century ago. However, although it is widely accepted that natural competence can contribute to the spread of genetic material among prokaryotes, the question remains whether this mode of HGT can foster the transfer of larger DNA regions or only transfers shorter fragments, given that extracellular DNA is often heavily fragmented...
April 27, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28453251/influence-of-manure-application-on-the-environmental-resistome-under-finnish-agricultural-practice-with-restricted-antibiotic-use
#17
Johanna Muurinen, Robert Stedtfeld, Antti Karkman, Katariina Pärnänen, James Tiedje, Marko Virta
The co-occurrence of antibiotic-resistance genes (ARGs) and mobile genetic elements (MGEs) in farm environments can potentially foster the development of antibiotic-resistant pathogens. We studied the resistome of Finnish dairy and swine farms where use of antibiotics is limited to treating bacterial infections and manure is only applied from April to September. The resistome of manure, soil, and tile drainage water from the ditch was investigated from the beginning of the growing season until forage harvest...
May 11, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28450881/line-insertion-polymorphisms-are-abundant-but-at-low-frequencies-across-populations-of-anolis-carolinensis
#18
Robert P Ruggiero, Yann Bourgeois, Stéphane Boissinot
Vertebrate genomes differ considerably in size and structure. Among the features that show the most variation is the abundance of Long Interspersed Nuclear Elements (LINEs). Mammalian genomes contain 100,000s LINEs that belong to a single clade, L1, and in most species a single family is usually active at a time. In contrast, non-mammalian vertebrates (fish, amphibians and reptiles) contain multiple active families, belonging to several clades, but each of them is represented by a small number of recently inserted copies...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28448614/obtaining-retrotransposon-sequences-analysis-of-their-genomic-distribution-and-use-of-retrotransposon-derived-genetic-markers-in-lentil-lens-culinaris-medik
#19
Rita Rey-Baños, Luis E Sáenz de Miera, Pedro García, Marcelino Pérez de la Vega
Retrotransposons with long terminal repeats (LTR-RTs) are widespread mobile elements in eukaryotic genomes. We obtained a total of 81 partial LTR-RT sequences from lentil corresponding to internal retrotransposon components and LTRs. Sequences were obtained by PCR from genomic DNA. Approximately 37% of the LTR-RT internal sequences presented premature stop codons, pointing out that these elements must be non-autonomous. LTR sequences were obtained using the iPBS technique which amplifies sequences between LTR-RTs...
2017: PloS One
https://www.readbyqxmd.com/read/28447635/a-chromosome-conformation-capture-ordered-sequence-of-the-barley-genome
#20
Martin Mascher, Heidrun Gundlach, Axel Himmelbach, Sebastian Beier, Sven O Twardziok, Thomas Wicker, Volodymyr Radchuk, Christoph Dockter, Pete E Hedley, Joanne Russell, Micha Bayer, Luke Ramsay, Hui Liu, Georg Haberer, Xiao-Qi Zhang, Qisen Zhang, Roberto A Barrero, Lin Li, Stefan Taudien, Marco Groth, Marius Felder, Alex Hastie, Hana Šimková, Helena Staňková, Jan Vrána, Saki Chan, María Muñoz-Amatriaín, Rachid Ounit, Steve Wanamaker, Daniel Bolser, Christian Colmsee, Thomas Schmutzer, Lala Aliyeva-Schnorr, Stefano Grasso, Jaakko Tanskanen, Anna Chailyan, Dharanya Sampath, Darren Heavens, Leah Clissold, Sujie Cao, Brett Chapman, Fei Dai, Yong Han, Hua Li, Xuan Li, Chongyun Lin, John K McCooke, Cong Tan, Penghao Wang, Songbo Wang, Shuya Yin, Gaofeng Zhou, Jesse A Poland, Matthew I Bellgard, Ljudmilla Borisjuk, Andreas Houben, Jaroslav Doležel, Sarah Ayling, Stefano Lonardi, Paul Kersey, Peter Langridge, Gary J Muehlbauer, Matthew D Clark, Mario Caccamo, Alan H Schulman, Klaus F X Mayer, Matthias Platzer, Timothy J Close, Uwe Scholz, Mats Hansson, Guoping Zhang, Ilka Braumann, Manuel Spannagl, Chengdao Li, Robbie Waugh, Nils Stein
Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution...
April 26, 2017: Nature
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