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Mobile genome element

Julian R Garneau, Ognjen Sekulovic, Bruno Dupuy, Olga Soutourina, Marc Monot, Louis-Charles Fortier
Clostridioides difficile (formerly Clostridium difficile) is a pathogenic bacterium displaying great genetic diversity. A significant proportion of this diversity is due to the presence of integrated prophages. Here, we provide an in-depth analysis of phiCD211, also known as phiCDIF1296T, the largest phage identified in C. difficile so far, with a genome of 131-kbp. It shares morphological and genomic similarity with other large siphophages like phage 949 infecting Lactococcus lactis and phage c-st infecting Clostridium botulinum...
November 17, 2017: Applied and Environmental Microbiology
Ariane Toussaint
Phage Mu is the paradigm of a growing family of bacteriophages that infect a wide range of bacterial species and replicate their genome by replicative transposition. This molecular process, which is used by other mobile genetic elements to move within genomes, involves the profound rearrangement of the host genome [chromosome(s) and plasmid(s)] and can be exploited for the genetic analysis of the host bacteria and the in vivo cloning of host genes. In this chapter we review Mu-derived constructs that optimize the phage as a series of genetic tools that could inspire the development of similarly efficient tools from other transposable phages for a large spectrum of bacteria...
2018: Methods in Molecular Biology
Yi-Neng Han, Yuan Li, Sheng-Qiang Xia, Yuan-Yuan Zhang, Jun-Hua Zheng, Wei Li
P-Element induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a type of noncoding RNAs (ncRNAs) and interact with PIWI proteins. piRNAs were primarily described in the germline, but emerging evidence revealed that piRNAs are expressed in a tissue-specific manner among multiple human somatic tissue types as well and play important roles in transposon silencing, epigenetic regulation, gene and protein regulation, genome rearrangement, spermatogenesis and germ stem-cell maintenance. PIWI proteins were first discovered in Drosophila and they play roles in spermatogenesis, germline stem-cell maintenance, self-renewal, retrotransposons silencing and the male germline mobility control...
November 3, 2017: Cellular Physiology and Biochemistry
Sébastien Matamoros, Jarne M van Hattem, Maris S Arcilla, Niels Willemse, Damian C Melles, John Penders, Trung Nguyen Vinh, Ngo Thi Hoa, Menno D de Jong, Constance Schultsz
To understand the dynamics behind the worldwide spread of the mcr-1 gene, we determined the population structure of Escherichia coli and of mobile genetic elements (MGEs) carrying the mcr-1 gene. After a systematic review of the literature we included 65 E. coli whole genome sequences (WGS), adding 6 recently sequenced travel related isolates, and 312 MLST profiles. We included 219 MGEs described in 7 Enterobacteriaceae species isolated from human, animal and environmental samples. Despite a high overall diversity, 2 lineages were observed in the E...
November 10, 2017: Scientific Reports
Silke Peter, Philipp Oberhettinger, Leonard Schuele, Ariane Dinkelacker, Wichard Vogel, Daniela Dörfel, Daniela Bezdan, Stephan Ossowski, Matthias Marschal, Jan Liese, Matthias Willmann
BACKGROUND: Pseudomonas putida is a Gram-negative, non-fermenting bacterium frequently encountered in various environmental niches. P. putida rarely causes disease in humans, though serious infections and outbreaks have been reported from time to time. Some have suggested that P. putida functions as an exchange platform for antibiotic resistance genes (ARG), and thus represents a serious concern in the spread of ARGs to more pathogenic organisms within a hospital. Though poorly understood, the frequency of ARG exchange between P...
November 10, 2017: BMC Genomics
Pieter Albers, Cédric Lood, Basak Özturk, Benjamin Horemans, Rob Lavigne, Vera van Noort, René De Mot, Kathleen Marchal, Aminael Sanchez-Rodriguez, Dirk Springael
Variovorax sp. WDL1 mediates hydrolysis of the herbicide linuron into 3,4-dichloroaniline (DCA) and N,O-dimethylhydroxylamine in a tripartite bacterial consortium with Comamonas testosteroni WDL7 and Hyphomicrobium sulfonivorans WDL6. Although strain WDL1 contains the dcaQTA1A2B operon for DCA oxidation, this conversion is mainly performed by WDL7. Phenotypic diversification observed in WDL1 cultures and scrutiny of the WDL1 genome suggest that WDL1 cultures consist of two dedicated subpopulations, i.e., a linuron-hydrolyzing subpopulation (Lin+DCA-) and a DCA-oxidizing subpopulation (Lin-DCA+)...
November 10, 2017: Environmental Microbiology
Modesto Redrejo-Rodríguez, Carlos D Ordóñez, Mónica Berjón-Otero, Juan Moreno-González, Cristian Aparicio-Maldonado, Patrick Forterre, Margarita Salas, Mart Krupovic
Family B DNA polymerases (PolBs) play a central role during replication of viral and cellular chromosomes. Here, we report the discovery of a third major group of PolBs, which we denote primer-independent PolB (piPolB), that might be a link between the previously known protein-primed and RNA/DNA-primed PolBs. PiPolBs are encoded by highly diverse mobile genetic elements, pipolins, integrated in the genomes of diverse bacteria and also present as circular plasmids in mitochondria. Biochemical characterization showed that piPolB displays efficient DNA polymerization activity that can use undamaged and damaged templates and is endowed with proofreading and strand displacement capacities...
November 7, 2017: Cell Reports
Yuki Wakabayashi, Kaoru Umeda, Shinya Yonogi, Hiromi Nakamura, Kaori Yamamoto, Yuko Kumeda, Kentaro Kawatsu
Staphylococcal food poisoning (SFP) is caused by staphylococcal enterotoxins (SEs) preformed in food materials. SE genes are encoded on mobile genetic elements and are widely found across Staphylococcus species including S. argenteus, although most SFP cases are caused by S. aureus. S. argenteus, recently discriminated from S. aureus as a novel species, are non-pigmented staphylococci phenotypically related to S. aureus. In 2014 and 2015, two independent food poisoning cases occurred in Osaka, Japan, in which non-pigmented staphylococci were predominantly isolated...
October 22, 2017: International Journal of Food Microbiology
Barun Pradhan, Tatiana Cajuso, Riku Katainen, Päivi Sulo, Tomas Tanskanen, Outi Kilpivaara, Esa Pitkänen, Lauri A Aaltonen, Liisa Kauppi, Kimmo Palin
Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. In most copy events, only the L1 sequence is inserted, however, they can also mobilize the flanking non-repetitive region by a process known as 3' transduction. L1 insertions can contribute to genome plasticity and cause potentially tumorigenic genomic instability. However, detecting the activity of a particular source L1 and identifying new insertions stemming from it is a challenging task with current methodological approaches...
November 6, 2017: Scientific Reports
Eiji Yokoyama, Shinichiro Hirai, Taichiro Ishige, Satoshi Murakami
Seventeen clusters of Shiga toxin-producing Escherichia coli O157:H7/- (O157) strains, determined by cluster analysis of pulsed-field gel electrophoresis patterns, were analyzed using whole genome sequence (WGS) data to investigate this pathogen's molecular epidemiology. The 17 clusters included 136 strains containing strains from nine outbreaks, with each outbreak caused by a single source contaminated with the organism, as shown by epidemiological contact surveys. WGS data of these strains were used to identify single nucleotide polymorphisms (SNPs) by two methods: short read data were directly mapped to a reference genome (mapping derived SNPs) and common SNPs between the mapping derived SNPs and SNPs in assembled data of short read data (common SNPs)...
October 17, 2017: International Journal of Food Microbiology
Yingzhou Xie, Yiqing Wei, Yue Shen, Xiaobin Li, Hao Zhou, Cui Tai, Zixin Deng, Hong-Yu Ou
TADB2.0 ( is an updated database that provides comprehensive information about bacterial type II toxin-antitoxin (TA) loci. Compared with the previous version, the database refined and the new data schema is employed. With the aid of text mining and manual curation, it recorded 6193 type II TA loci in 870 replicons of bacteria and archaea, including 105 experimentally validated TA loci. In addition, the newly developed tool TAfinder combines the homolog searches and the operon structure detection, allowing the prediction for type II TA pairs in bacterial genome sequences...
November 2, 2017: Nucleic Acids Research
Muluneh Tamiru, Thomas J Hardcastle, Mathew G Lewsey
Contents I. II. III. IV. V. VI. VII. VIII. IX. References SUMMARY: RNA-directed DNA methylation (RdDM) at cytosine residues regulates gene expression, silences transposable elements and influences genome stability. The mechanisms responsible for RdDM are guided to target loci by small RNAs (sRNAs) that can move within plants cell to cell and long distance. Here we discuss recent advances in the understanding of interactions between mobile sRNAs and DNA methylation. We describe the mechanisms of sRNA movement, the differences between known classes of mobile sRNA-DNA methylation interactions and the limits of current knowledge...
November 6, 2017: New Phytologist
Richard P Novick, Geeta Ram
The staphylococcal pathogenicity islands (SaPIs) are highly mobile 15kb genomic islands that carry superantigen genes and other virulence factors and are mobilized by helper phages. Helper phages counteract the SaPI repressor to induce the SaPI replication cycle, resulting in encapsidation in phage like particles, enabling high frequency transfer. The SaPIs split from a protophage lineage in the distant past, have evolved a variety of novel and salient features, and have become an invaluable component of the staphylococcal genome...
October 31, 2017: Current Opinion in Microbiology
Laurence Van Melderen, Dukas Jurenas, Abel Garcia-Pino
Toxin---antitoxin systems (TA) are widespread in bacteria and archea. They are commonly found in chromosomes and mobile genetic elements. These systems move from different genomic locations and bacterial hosts through horizontal gene transfer, using mobile elements as vehicles. Their potential roles in bacterial physiology are still a matter of debate in the field. The mechanisms of action of different toxin families have been deciphered at the molecular level. Intriguingly, the vast majority of these toxins target protein synthesis...
November 3, 2017: RNA Biology
Diego H Sanchez, Hervé Gaubert, Hajk-Georg Drost, Nicolae Radu Zabet, Jerzy Paszkowski
Retrotransposons containing long terminal repeats (LTRs) form a substantial fraction of eukaryotic genomes. The timing of past transposition can be estimated by quantifying the accumulation of mutations in initially identical LTRs. This way, retrotransposons are divided into young, potentially mobile elements, and old that moved thousands or even millions of years ago. Both types are found within a single retrotransposon family and it is assumed that the old members will remain immobile and degenerate further...
November 3, 2017: Nature Communications
Samantha J Hau, Darrell O Bayles, David P Alt, Tracy L Nicholson
Methicillin-resistant Staphylococcus aureus (MRSA) can be a commensal or pathogen in humans. Pathogenicity and disease are related to the acquisition of mobile genetic elements encoding virulence and antimicrobial resistance genes. Here, we report draft genome sequences for 50 clinical MRSA isolates from humans with MRSA-related disease.
November 2, 2017: Genome Announcements
Samantha J Hau, Darrell O Bayles, David P Alt, Timothy S Frana, Tracy L Nicholson
Methicillin-resistant Staphylococcus aureus colonizes humans and other animals such as swine. Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) sequence type 5 (ST5) isolates are a public concern due to their pathogenicity and ability to acquire mobile genetic elements. This report presents draft genome sequences for 63 LA-MRSA ST5 isolates in the United States.
November 2, 2017: Genome Announcements
Evgenii I Olekhnovich, Artem T Vasilyev, Vladimir I Ulyantsev, Elena S Kostryukova, Alexander V Tyakht
Motivation: Antibiotic resistance is an important global public health problem. Human gut microbiota is an accumulator of resistance genes potentially providing them to pathogens. It is important to develop tools for identifying the mechanisms of how resistance is transmitted between gut microbial species and pathogens. Results: We developed MetaCherchant - an algorithm for extracting the genomic environment of antibiotic resistance genes from metagenomic data in the form of a graph...
October 28, 2017: Bioinformatics
Andreas E Zautner, Boyke Bunk, Yvonne Pfeifer, Cathrin Spröer, Utz Reichard, Helmut Eiffert, Simone Scheithauer, Uwe Groß, Jörg Overmann, Wolfgang Bohne
Objectives: Carbapenemase-producing Klebsiella pneumoniae pose an increasing risk for healthcare facilities worldwide. A continuous monitoring of ST distribution and its association with resistance and virulence genes is required for early detection of successful K. pneumoniae lineages. In this study, we used WGS to characterize MDR blaOXA-48-positive K. pneumoniae isolated from inpatients at the University Medical Center Göttingen, Germany, between March 2013 and August 2014. Methods: Closed genomes for 16 isolates of carbapenemase-producing K...
October 1, 2017: Journal of Antimicrobial Chemotherapy
Pawan Kumar, Satyabrata Bag, Tarini Shankar Ghosh, Prasanta Dey, Mayanka Dayal, Bipasa Saha, Jyoti Verma, Archana Pant, Shruti Saxena, Anbumani Desigamani, Preety Rana, Dhirendra Kumar, Naresh C Sharma, Pranita Hanpude, Tushar K Maiti, Asish K Mukhopadhyay, Rupak K Bhadra, G Balakrish Nair, Thandavarayan Ramamurthy, Bhabatosh Das
Emergence of antimicrobial resistant Gram-negative bacteria has created a serious global health crisis and threatens the effectiveness of most, if not all, antibiotics commonly used to prevent and treat bacterial infections. There is a dearth of detailed studies on the prevalence of antimicrobial resistance (AMR) patterns in India. Here, we have isolated and examined AMR patterns of 654 enteric pathogens and investigated complete genome sequences of isolates from six representative genera, which in aggregate encode resistance against 22 antibiotics representing nine distinct drug classes...
October 31, 2017: Scientific Reports
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