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https://www.readbyqxmd.com/read/29775460/genus-wide-comparison-of-pseudovibrio-bacterial-genomes-reveal-diverse-adaptations-to-different-marine-invertebrate-hosts
#1
Anoop Alex, Agostinho Antunes
Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater...
2018: PloS One
https://www.readbyqxmd.com/read/29774045/transposon-derived-non-coding-rnas-and-their-function-in-plants
#2
REVIEW
Jungnam Cho
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans -acting regulatory roles of TE-derived RNAs have been rarely studied...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29771354/methylation-guide-rna-evolution-in-archaea-structure-function-and-genomic-organization-of-110-c-d-box-srna-families-across-six-pyrobaculum-species
#3
Lauren M Lui, Andrew V Uzilov, David L Bernick, Andrea Corredor, Todd M Lowe, Patrick P Dennis
Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29766687/structured-illumination-to-spatially-map-chromatin-motions
#4
Keith Bonin, Amanda Smelser, Naike Salvador Moreno, George Holzwarth, Kevin Wang, Preston Levy, Pierre-Alexandre Vidi
We describe a simple optical method that creates structured illumination of a photoactivatable probe and apply this method to characterize chromatin motions in nuclei of live cells. A laser beam coupled to a diffractive optical element at the back focal plane of an excitation objective generates an array of near diffraction-limited beamlets with FWHM of 340  ±  30  nm, which simultaneously photoactivate a 7  ×  7 matrix pattern of GFP-labeled histones, with spots 1.70  μm apart. From the movements of the photoactivated spots, we map chromatin diffusion coefficients at multiple microdomains of the cell nucleus...
May 2018: Journal of Biomedical Optics
https://www.readbyqxmd.com/read/29763462/the-annotation-of-repetitive-elements-in-the-genome-of-channel-catfish-ictalurus-punctatus
#5
Zihao Yuan, Tao Zhou, Lisui Bao, Shikai Liu, Huitong Shi, Yujia Yang, Dongya Gao, Rex Dunham, Geoff Waldbieser, Zhanjiang Liu
Channel catfish (Ictalurus punctatus) is a highly adaptive species and has been used as a research model for comparative immunology, physiology, and toxicology among ectothermic vertebrates. It is also economically important for aquaculture. As such, its reference genome was generated and annotated with protein coding genes. However, the repetitive elements in the catfish genome are less well understood. In this study, over 417.8 Megabase (MB) of repetitive elements were identified and characterized in the channel catfish genome...
2018: PloS One
https://www.readbyqxmd.com/read/29743957/the-case-for-not-masking-away-repetitive-dna
#6
EDITORIAL
R Keith Slotkin
In the course of analyzing whole-genome data, it is common practice to mask or filter out repetitive regions of a genome, such as transposable elements and endogenous retroviruses, in order to focus only on genes and thus simplify the results. This Commentary is a plea from one member of the Mobile DNA community to all gene-centric researchers: please do not ignore the repetitive fraction of the genome . Please stop narrowing your findings by only analyzing a minority of the genome, and instead broaden your analyses to include the rich biology of repetitive and mobile DNA...
2018: Mobile DNA
https://www.readbyqxmd.com/read/29743642/genomic-epidemiology-of-shigella-in-the-united-kingdom-shows-transmission-of-pathogen-sublineages-and-determinants-of-antimicrobial-resistance
#7
Kate S Baker, Timothy J Dallman, Nigel Field, Tristan Childs, Holly Mitchell, Martin Day, François-Xavier Weill, Sophie Lefèvre, Mathieu Tourdjman, Gwenda Hughes, Claire Jenkins, Nicholas Thomson
Shigella are globally important diarrhoeal pathogens that are endemic in low-to-middle income nations and also occur in high income nations, typically in travellers or community-based risk-groups. Shigella phylogenetics reveals population structures that are more reliable than those built with traditional typing methods, and has identified sublineages associated with specific geographical regions or patient groups. Genomic analyses reveal temporal increases in Shigella antimicrobial resistance (AMR) gene content, which is frequently encoded on mobile genetic elements...
May 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29743038/valine-glutamine-vq-motif-coding-genes-are-ancient-and-non-plant-specific-with-comprehensive-expression-regulation-by-various-biotic-and-abiotic-stresses
#8
Shu-Ye Jiang, Mayalagu Sevugan, Srinivasan Ramachandran
BACKGROUND: Valine-glutamine (VQ) motif containing proteins play important roles in abiotic and biotic stress responses in plants. However, little is known about the origin and evolution as well as comprehensive expression regulation of the VQ gene family. RESULTS: In this study, we systematically surveyed this gene family in 50 plant genomes from algae, moss, gymnosperm and angiosperm and explored their presence in other species from animals, bacteria, fungi and viruses...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29739668/whole-genome-comparison-of-high-and-low-virulent-staphylococcus-aureus-isolates-inducing-implant-associated-bone-infections
#9
Gopala Krishna Mannala, Julian Koettnitz, Walid Mohamed, Ursula Sommer, Katrin Susanne Lips, Cathrin Spröer, Boyke Bunk, Jörg Overmann, Torsten Hain, Christian Heiss, Eugen Domann, Volker Alt
Staphylococcus aureus can cause wide range of infections from simple soft skin infections to severe endocarditis, bacteremia, osteomyelitis and implant associated bone infections (IABI). The focus of the present investigation was to study virulence properties of S. aureus isolates from acute and chronic IABI by means of their in vivo lethality, in vitro osteoblasts invasion, biofilm formation and subsequently whole genome comparison between high and low virulent strains. Application of insect infection model Galleria mellonella revealed high, intermediate and low virulence phenotypes of these clinical isolates, which showed good correlation with osteoblast invasion and biofilm formation assays...
April 25, 2018: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/29739320/mobilization-of-retrotransposons-as-a-cause-of-chromosomal-diversification-and-rapid-speciation-the-case-for-the-antarctic-teleost-genus-trematomus
#10
J Auvinet, P Graça, L Belkadi, L Petit, E Bonnivard, A Dettaï, W H Detrich, C Ozouf-Costaz, D Higuet
BACKGROUND: The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment to understanding the roles of TEs in genome evolution is the lack of comparative and integrative analyses on complete taxonomic groups. To help overcome this problem, we have focused on the Antarctic teleost genus Trematomus (Notothenioidei: Nototheniidae), as they experienced rapid speciation accompanied by dramatic chromosomal diversity...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29738683/argonaute-proteins-and-mechanisms-of-rna-interference-in-eukaryotes-and-prokaryotes
#11
REVIEW
A V Olina, A V Kulbachinskiy, A A Aravin, D M Esyunina
Noncoding RNAs play essential roles in genetic regulation in all organisms. In eukaryotic cells, many small noncoding RNAs act in complex with Argonaute proteins and regulate gene expression by recognizing complementary RNA targets. The complexes of Argonaute proteins with small RNAs also play a key role in silencing of mobile genetic elements and, in some cases, viruses. These processes are collectively called RNA interference. RNA interference is a powerful tool for specific gene silencing in both basic research and therapeutic applications...
May 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29717009/an-attenuated-crispr-cas-system-in-enterococcus-faecalis-permits-dna-acquisition
#12
Karthik Hullahalli, Marinelle Rodrigues, Uyen Thy Nguyen, Kelli Palmer
Antibiotic-resistant bacteria are critical public health concerns. Among the prime causative factors for the spread of antibiotic resistance is horizontal gene transfer (HGT). A useful model organism for investigating the relationship between HGT and antibiotic resistance is the opportunistic pathogen Enterococcus faecalis , since the species possesses highly conjugative plasmids that readily disseminate antibiotic resistance genes and virulence factors in nature. Unlike many commensal E. faecalis strains, the genomes of multidrug-resistant (MDR) E...
May 1, 2018: MBio
https://www.readbyqxmd.com/read/29716961/whole-genome-sequence-and-comparative-genomics-analysis-of-multi-drug-resistant-environmental-staphylococcus-epidermidis-st59
#13
Zhen Xu, Raju Misra, Dorota Jamrozy, Gavin K Paterson, Ronald R Cutler, Mark A Holmes, Saheer Gharbia, Hermine V Mkrtchyan
Staphylococcus epidermidis is a major opportunistic pathogen primarily recovered from device-associated healthcare associated infections (DA-HAIs). Although S. epidermidis and other coagulase-negative staphylococci (CoNS) are less virulent than Staphylococcus aureus , these bacteria are an important reservoir of antimicrobial resistance genes and resistance-associated mobile genetic elements that can be transferred between staphylococcal species. We report a whole genome sequence of a multidrug resistant S...
April 30, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29715483/deciphering-the-genomes-of-16-acanthamoeba-species-does-not-provide-evidence-of-integration-of-known-giant-virus-associated-mobile-genetic-elements
#14
Nisrine Chelkha, Philippe Colson, Anthony Levasseur, Bernard La Scola
Giant viruses infect protozoa, especially amoebae of the genus Acanthamoeba. These viruses possess genetic elements named Mobilome. So far, this mobilome comprises provirophages which are integrated into the genome of their hosts, transpovirons, and Maverick/Polintons. Virophages replicate inside virus factories within Acanthamoeba and can decrease the infectivity of giant viruses. The virophage infecting CroV was found to be integrated in the host of CroV, Cafeteria roenbergensis, thus protecting C. roenbergensis by reduction of CroV multiplication...
April 28, 2018: Virus Research
https://www.readbyqxmd.com/read/29705597/transposable-elements-all-mobile-all-different-some-stress-responsive-some-adaptive
#15
REVIEW
Sophie Lanciano, Marie Mirouze
Transposable elements (TEs) were first identified through the polymorphisms they induced in plants and animals. Genomic studies have later revealed that TEs were highly abundant in eukaryotic genomes. Recently, more precise single individual genomic analyses have unravelled the huge diversity of TE insertions in many plant and animal species. In most cases the stress conditions behind this diversity are not known and neither is the adaptive capacity of these natural TE-induced variants. Here, we review some of the most recent examples of TE-related impacts on gene expression at the locus or the genome level and discuss the rich diversity of the TE repertoire and its potential role in adaptive evolution...
April 26, 2018: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/29697183/genome-biology-of-a-novel-lineage-of-planctomycetes-widespread-in-anoxic-aquatic-environments
#16
Stefan Spring, Boyke Bunk, Cathrin Spröer, Manfred Rohde, Hans-Peter Klenk
Anaerobic strains affiliated with a novel order-level lineage of the Phycisphaerae class were retrieved from the suboxic zone of a hypersaline cyanobacterial mat and anoxic sediments of solar salterns. Genome sequences of five isolates were obtained and compared with metagenome-assembled genomes representing related uncultured bacteria from various anoxic aquatic environments. Gene content surveys suggest a strictly fermentative saccharolytic metabolism for members of this lineage, which could be confirmed by the phenotypic characterization of isolates...
April 26, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29692414/a-to-i-rna-editing-immune-protector-and-transcriptome-diversifier
#17
REVIEW
Eli Eisenberg, Erez Y Levanon
Modifications of RNA affect its function and stability. RNA editing is unique among these modifications because it not only alters the cellular fate of RNA molecules but also alters their sequence relative to the genome. The most common type of RNA editing is A-to-I editing by double-stranded RNA-specific adenosine deaminase (ADAR) enzymes. Recent transcriptomic studies have identified a number of 'recoding' sites at which A-to-I editing results in non-synonymous substitutions in protein-coding sequences. Many of these recoding sites are conserved within (but not usually across) lineages, are under positive selection and have functional and evolutionary importance...
April 24, 2018: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/29691340/extensive-gene-amplification-as-a-mechanism-for-piperacillin-tazobactam-resistance-in-escherichia-coli
#18
Lisa M Schechter, David P Creely, Cherilyn D Garner, Dee Shortridge, Hoan Nguyen, Lei Chen, Blake M Hanson, Erica Sodergren, George M Weinstock, W Michael Dunne, Alex van Belkum, Shana R Leopold
Although the TEM-1 β-lactamase (BlaTEM-1 ) hydrolyzes penicillins and narrow-spectrum cephalosporins, organisms expressing this enzyme are typically susceptible to β-lactam/β-lactamase inhibitor combinations such as piperacillin-tazobactam (TZP). However, our previous work led to the discovery of 28 clinical isolates of Escherichia coli resistant to TZP that contained only bla TEM-1 One of these isolates, E. coli 907355, was investigated further in this study. E. coli 907355 exhibited significantly higher β-lactamase activity and BlaTEM-1 protein levels when grown in the presence of subinhibitory concentrations of TZP...
April 24, 2018: MBio
https://www.readbyqxmd.com/read/29691332/clinically-relevant-plasmid-host-interactions-indicate-that-transcriptional-and-not-genomic-modifications-ameliorate-fitness-costs-of-klebsiella-pneumoniae-carbapenemase-carrying-plasmids
#19
Michelle M C Buckner, Howard T H Saw, Rachael N Osagie, Alan McNally, Vito Ricci, Matthew E Wand, Neil Woodford, Alasdair Ivens, Mark A Webber, Laura J V Piddock
The rapid dissemination of antimicrobial resistance (AMR) around the globe is largely due to mobile genetic elements, such as plasmids. They confer resistance to critically important drugs, including extended-spectrum beta-lactams, carbapenems, and colistin. Large, complex resistance plasmids have evolved alongside their host bacteria. However, much of the research on plasmid-host evolution has focused on small, simple laboratory plasmids in laboratory-adapted bacterial hosts. These and other studies have documented mutations in both host and plasmid genes which occur after plasmid introduction to ameliorate fitness costs of plasmid carriage...
April 24, 2018: MBio
https://www.readbyqxmd.com/read/29684486/contribution-of-transposable-elements-in-the-plant-s-genome
#20
REVIEW
Mahbod Sahebi, Mohamed M Hanafi, Andre J van Wijnen, David Rice, M Y Rafii, Parisa Azizi, Mohamad Osman, Sima Taheri, Mohd Faizal Abu Bakar, Mohd Noor Mat Isa, Yusuf Muhammad Noor
Plants maintain extensive growth flexibility under different environmental conditions, allowing them to continuously and rapidly adapt to alterations in their environment. A large portion of many plant genomes consists of transposable elements (TEs) that create new genetic variations within plant species. Different types of mutations may be created by TEs in plants. Many TEs can avoid the host's defense mechanisms and survive alterations in transposition activity, internal sequence and target site. Thus, plant genomes are expected to utilize a variety of mechanisms to tolerate TEs that are near or within genes...
April 20, 2018: Gene
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