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Mobile genome element

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https://www.readbyqxmd.com/read/28645177/mobile-genetic-elements-in-neisseria-gonorrhoeae-movement-for-change
#1
Ana Cehovin, Steven B Lewis
Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhoeae, possesses several mobile genetic elements (MGEs). The MGEs such as transposable elements mediate intra-chromosomal rearrangements, while plasmids and the gonococcal genetic island are involved in inter-chromosomal gene transfer. Additionally, gonococcal MGEs serve as hotspots for recombination and integration of other genetic elements such as bacteriophages, contribute to gene regulation or spread genes through gonococcal populations by horizontal gene transfer...
June 22, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28644125/exploiting-crispr-cas-to-manipulate-enterococcus-faecalis-populations
#2
Karthik Hullahalli, Marinelle Rodrigues, Kelli L Palmer
CRISPR-Cas provides a barrier to horizontal gene transfer in prokaryotes. It was previously observed that functional CRISPR-Cas systems are absent from multidrug-resistant (MDR) Enterococcus faecalis, which only possess an orphan CRISPR locus, termed CRISPR2, lacking cas genes. It was of interest to investigate how the interplay between CRISPR-Cas genome defense and antibiotic selection for mobile genetic elements shapes E. faecalis populations. Here, we demonstrate that CRISPR2 can be reactivated for genome defense in MDR strains...
June 23, 2017: ELife
https://www.readbyqxmd.com/read/28642863/friends-enemies-endogenous-retroviruses-are-major-transcriptional-regulators-of-human-dna
#3
REVIEW
Anton A Buzdin, Vladimir Prassolov, Andrew V Garazha
Endogenous retroviruses are mobile genetic elements hardly distinguishable from infectious, or "exogenous," retroviruses at the time of insertion in the host DNA. Human endogenous retroviruses (HERVs) are not rare. They gave rise to multiple families of closely related mobile elements that occupy ~8% of the human genome. Together, they shape genomic regulatory landscape by providing at least ~320,000 human transcription factor binding sites (TFBS) located on ~110,000 individual HERV elements. The HERVs host as many as 155,000 mapped DNaseI hypersensitivity sites, which denote loci active in the regulation of gene expression or chromatin structure...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28642606/transposable-elements-in-cancer
#4
REVIEW
Kathleen H Burns
Transposable elements give rise to interspersed repeats, sequences that comprise most of our genomes. These mobile DNAs have been historically underappreciated - both because they have been presumed to be unimportant, and because their high copy number and variability pose unique technical challenges. Neither impediment now seems steadfast. Interest in the human mobilome has never been greater, and methods enabling its study are maturing at a fast pace. This Review describes the activity of transposable elements in human cancers, particularly long interspersed element-1 (LINE-1)...
July 2017: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/28642158/genetic-diversity-of-environmental-vibrio-cholerae-o1-strains-isolated-in-northern-vietnam
#5
Taichiro Takemura, Kazunori Murase, Fumito Maruyama, Tran Thi Luong, Atsushi Ota, Ichiro Nakagawa, Nguyen Dong Tu, Ngo Tu Cuong, Nguyen Thi Hang, Asako Tokizawa, Masatomo Morita, Makoto Ohnishi, Nguyen Binh Minh, Tetsu Yamashiro
Cholera epidemics have been recorded periodically in Vietnam during the seventh cholera pandemic. Since cholera is a water-borne disease, systematic monitoring of environmental waters for Vibrio cholerae presence is important for predicting and preventing cholera epidemics. We conducted monitoring, isolation, and genetic characterization of V. cholerae strains in Nam Dinh province of Northern Vietnam from Jul 2013 to Feb 2015. In this study, four V. cholerae O1 strains were detected and isolated from 110 analyzed water samples (3...
June 19, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28642157/genome-comparisons-of-two-taiwanese-community-associated-methicillin-resistant-staphylococcus-aureus-st59-clones-support-the-multi-origin-theory-of-ca-mrsa
#6
Ye Feng, Hsiu-Ling Chen, Chih-Jung Chen, Chyi-Liang Chen, Cheng-Hsun Chiu
Sequence type (ST) 59 is an epidemic lineage of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) in Asia. Two ST59 clones are prevalent in Taiwan: the Taiwan clone (TW) causes severe infections, whereas the Asian-Pacific clone (AP) is usually commensal. In this study, we sequenced the genome and transcriptome of the representative strains of these two clones and found their differences to focus on three mobile genetic elements: TW carries SCCmec Type VT, Panton-Valentine leucocidin (PVL)-encoding prophage ΦSa2, whereas AP carries SCCmec Type IV and staphylokinase (SAK)-encoding prophage ΦSa3...
June 19, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28637205/evolution-and-comparative-genomics-of-paqu-like-conjugative-plasmids-in-vibrio-species
#7
Ruichao Li, Lianwei Ye, Marcus Ho Yin Wong, Zhiwei Zheng, Edward Wai Chi Chan, Sheng Chen
Objectives: To investigate a set of MDR conjugative plasmids found in Vibrio species and characterize the underlying evolution process. Methods: pAQU-type plasmids from Vibrio species were sequenced using both Illumina and PacBio platforms. Bioinformatics tools were utilized to analyse the typical MDR regions and core genes in the plasmids. Results: The nine pAQU-type plasmids ranged from ∼160 to 206 kb in size and were found to harbour as many as 111 core genes encoding conjugative, replication and maintenance functions...
June 20, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28633403/structured-populations-of-sulfolobus-acidocaldarius-with-susceptibility-to-mobile-genetic-elements
#8
Rika E Anderson, Angela Kouris, Christopher H Seward, Kate M Campbell, Rachel J Whitaker
The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28630130/how-a-genetically-stable-extremophile-evolves-modes-of-genome-diversification-in-the-archaeon-sulfolobus-acidocaldarius
#9
Dominic Mao, Dennis W Grogan
In order to analyze in molecular terms how Sulfolobus genomes diverge, damage-induced mutations and natural polymorphisms (PMs) were identified in laboratory constructs and wild-type isolates, respectively, of Sulfolobus acidocaldarius Among wild-type isolates drawn from one local population, pairwise nucleotide divergence averaged 4 x 10(-6), which is about 0.15% of the corresponding divergence reported for Sulfolobus islandicus The most variable features of wild-type S. acidocaldarius genomes were homopolymer (mononucleotide) tracts and longer tandem repeats, consistent with the spontaneous mutations that occur under laboratory conditions...
June 19, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28630115/discovering-complete-quasispecies-in-bacterial-genomes
#10
Frederic Bertels, Chaitanya S Gokhale, Arne Traulsen
Mobile genetic elements can be found in almost all genomes. Possibly the most common non-autonomous mobile genetic elements in bacteria are REPINs that can occur hundreds of times within a genome. The sum of all REPINs in a genome can be viewed as an evolving population because REPINs replicate and mutate. In contrast to most other biological populations, we know the exact composition of the REPIN population and the sequence of each member of the population. Here, we model the evolution of REPINs as quasispecies...
June 19, 2017: Genetics
https://www.readbyqxmd.com/read/28628615/flipping-chromosomes-in-deep-sea-archaea
#11
Matteo Cossu, Catherine Badel, Ryan Catchpole, Danièle Gadelle, Evelyne Marguet, Valérie Barbe, Patrick Forterre, Jacques Oberto
One of the major mechanisms driving the evolution of all organisms is genomic rearrangement. In hyperthermophilic Archaea of the order Thermococcales, large chromosomal inversions occur so frequently that even closely related genomes are difficult to align. Clearly not resulting from the native homologous recombination machinery, the causative agent of these inversions has remained elusive. We present a model in which genomic inversions are catalyzed by the integrase enzyme encoded by a family of mobile genetic elements...
June 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28615283/cis-and-trans-regulatory-effects-on-gene-expression-in-a-natural-population-of-drosophila-melanogaster
#12
Naoki Osada, Ryutaro Miyagi, Aya Takahashi
Cis- and trans-regulatory mutations are important contributors to transcriptome evolution. Quantifying their relative contributions to intraspecific variation in gene expression is essential for understanding the population genetic processes that underlie evolutionary changes in gene expression. Here, we have examined this issue by quantifying genome-wide allele specific expression (ASE) variation using a crossing scheme that produces F1 hybrids between 18 different Drosophila melanogaster strains sampled from the Drosophila Genetic Reference Panel (DGRP) and a reference strain from another population...
June 14, 2017: Genetics
https://www.readbyqxmd.com/read/28614915/identification-of-an-enhancer-critical-for-the-ephirn-a5-gene-expression-in-the-posterior-region-of-the-mesencephalon
#13
Eunjeong Park, Hyuna Noh, Soochul Park
Ephrin-A5 has been implicated in the regulation of brain morphogenesis and axon pathfinding. In this study, we used bacterial homologous recombination to express a LacZ reporter in various ephrin-A5 BAC clones to identify elements that regulate ephrin-A5 gene expression during mesencephalon development. We found that there is mesencephalonspecific enhancer activity localized to a specific +25.0 kb to +30.5 kb genomic region in the first intron of ephrin-A5. Further comparative genomic analysis indicated that two evolutionary conserved regions, ECR1 and ECR2, were present within this 5...
June 13, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28611826/the-evolution-of-bacterial-genome-architecture
#14
REVIEW
Louis-Marie Bobay, Howard Ochman
The genome architecture of bacteria and eukaryotes evolves in opposite directions when subject to genetic drift, a difference that can be ascribed to the fact that bacteria exhibit a mutational bias that deletes superfluous sequences, whereas eukaryotes are biased toward large insertions. Expansion of eukaryotic genomes occurs through the addition of non-functional sequences, such as repetitive sequences and transposable elements, whereas variation in bacterial genome size is largely due to the acquisition and loss of functional accessory genes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28611742/analysis-of-the-genome-and-mobilome-of-a-dissimilatory-arsenate-reducing-aeromonas-sp-o23a-reveals-multiple-mechanisms-for-heavy-metal-resistance-and-metabolism
#15
Witold Uhrynowski, Przemyslaw Decewicz, Lukasz Dziewit, Monika Radlinska, Pawel S Krawczyk, Leszek Lipinski, Dorota Adamska, Lukasz Drewniak
Aeromonas spp. are among the most ubiquitous microorganisms, as they have been isolated from different environmental niches including waters, soil, as well as wounds and digestive tracts of poikilothermic animals and humans. Although much attention has been paid to the pathogenicity of Aeromonads, the role of these bacteria in environmentally important processes, such as transformation of heavy metals, remains to be discovered. Therefore, the aim of this study was a detailed genomic characterization of Aeromonas sp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28606835/identification-and-characterization-of-mobile-genetic-elements-lines-from-brassica-genome
#16
Faisal Nouroz, Shumaila Noreen, Muhammad Fiaz Khan, Shehzad Ahmed, J S Pat Heslop-Harrison
Among transposable elements (TEs), the LTR retrotransposons are abundant followed by non-LTR retrotransposons in plant genomes, the lateral being represented by LINEs and SINEs. Computational and molecular approaches were used for the characterization of Brassica LINEs, their diversity and phylogenetic relationships. Four autonomous and four non-autonomous LINE families were identified and characterized from Brassica. Most of the autonomous LINEs displayed two open reading frames, ORF1 and ORF2, where ORF1 is a gag protein domain, while ORF2 encodes endonuclease (EN) and a reverse transcriptase (RT)...
June 9, 2017: Gene
https://www.readbyqxmd.com/read/28605718/diversity-classification-and-evolution-of-crispr-cas-systems
#17
REVIEW
Eugene V Koonin, Kira S Makarova, Feng Zhang
The bacterial and archaeal CRISPR-Cas systems of adaptive immunity show remarkable diversity of protein composition, effector complex structure, genome locus architecture and mechanisms of adaptation, pre-CRISPR (cr)RNA processing and interference. The CRISPR-Cas systems belong to two classes, with multi-subunit effector complexes in Class 1 and single-protein effector modules in Class 2. Concerted genomic and experimental efforts on comprehensive characterization of Class 2 CRISPR-Cas systems led to the identification of two new types and several subtypes...
June 9, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28602637/inhibition-mechanism-of-an-anti-crispr-suppressor-acriia4-targeting-spycas9
#18
Hui Yang, Dinshaw J Patel
Prokaryotic CRISPR-Cas adaptive immune systems utilize sequence-specific RNA-guided endonucleases to defend against infection by viruses, bacteriophages, and mobile elements, while these foreign genetic elements evolve diverse anti-CRISPR proteins to overcome the CRISPR-Cas-mediated defense of the host. Recently, AcrIIA2 and AcrIIA4, encoded by Listeria monocytogene prophages, were shown to block the endonuclease activity of type II-A Streptococcus pyogene Cas9 (SpyCas9). We now report the crystal structure of AcrIIA4 in complex with single-guide RNA-bound SpyCas9, thereby establishing that AcrIIA4 preferentially targets critical residues essential for PAM duplex recognition, as well as blocks target DNA access to key catalytic residues lining the RuvC pocket...
June 2, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28596783/analysis-of-ef-hand-proteins-in-soybean-genome-suggests-their-potential-roles-in-environmental-and-nutritional-stress-signaling
#19
Houqing Zeng, Yaxian Zhang, Xiajun Zhang, Erxu Pi, Yiyong Zhu
Calcium ion (Ca(2+)) is a universal second messenger that plays a critical role in plant responses to diverse physiological and environmental stimuli. The stimulus-specific signals are perceived and decoded by a series of Ca(2+) binding proteins serving as Ca(2+) sensors. The majority of Ca(2+) sensors possess the EF-hand motif, a helix-loop-helix structure which forms a turn-loop structure. Although EF-hand proteins in model plant such as Arabidopsis have been well described, the identification, classification, and the physiological functions of EF-hand-containing proteins from soybean are not systemically reported...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28594826/a-highly-specific-phage-defense-system-is-a-conserved-feature-of-the-vibrio-cholerae-mobilome
#20
Brendan J O'Hara, Zachary K Barth, Amelia C McKitterick, Kimberley D Seed
Vibrio cholerae-specific bacteriophages are common features of the microbial community during cholera infection in humans. Phages impose strong selective pressure that favors the expansion of phage-resistant strains over their vulnerable counterparts. The mechanisms allowing virulent V. cholerae strains to defend against the ubiquitous threat of predatory phages have not been established. Here, we show that V. cholerae PLEs (phage-inducible chromosomal island-like elements) are widespread genomic islands dedicated to phage defense...
June 8, 2017: PLoS Genetics
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