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N Shrestha, P H Weber, S V Burke, W Wysocki, M R Duvall, J J Bujarski
Although RNA viruses evolved the mechanisms of specific encapsidation, miss-packaging of cellular RNAs has been reported in such RNA virus systems as flock house virus or cucumber necrosis virus. To find out if brome mosaic virus (BMV), a tripartite RNA virus, can package cellular RNAs, BMV was propagated in barley and in Nicotiana benthamiana hosts, purified by cesium chloride (CsCl) gradient ultracentrifugation followed by nuclease treatment to remove any contaminating cellular (host) RNAs. The extracted virion RNA was then sequenced by using next-generation sequencing (NGS RNA-Seq) with the Illumina protocol...
May 10, 2018: Virus Research
Conghui Liu, Bo Liu, Yan Zhang, Fan Jiang, Yuwei Ren, Shuqu Li, Hengchao Wang, Wei Fan
Horizontal gene transfer (HGT), a mechanism that shares genetic material between the host and donor from separated offspring branches, has been described as a means of producing novel and beneficial phenotypes for the host organisms. However, in molluscs, the second most diverse group, the existence of HGT is still controversial. In the present study, 12 HGT genes were identified from California two-spot octopus Octopus bimaculoides based on a similarity search, phylogenetic construction, gene composition analysis and PCR (Polymerase Chain Reaction) validation...
May 5, 2018: Gene
Frederick Johannes Clasen, Rian Ewald Pierneef, Bernard Slippers, Oleg Reva
BACKGROUND: Genomic islands (GIs) are inserts of foreign DNA that have potentially arisen through horizontal gene transfer (HGT). There are evidences that GIs can contribute significantly to the evolution of prokaryotes. The acquisition of GIs through HGT in eukaryotes has, however, been largely unexplored. In this study, the previously developed GI prediction tool, SeqWord Gene Island Sniffer (SWGIS), is modified to predict GIs in eukaryotic chromosomes. Artificial simulations are used to estimate ratios of predicting false positive and false negative GIs by inserting GIs into different test chromosomes and performing the SWGIS v2...
May 3, 2018: BMC Genomics
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
Kujin Tang, Yang Young Lu, Fengzhu Sun
Horizontal gene transfer (HGT) plays an important role in the evolution of microbial organisms including bacteria. Alignment-free methods based on single genome compositional information have been used to detect HGT. Currently, Manhattan and Euclidean distances based on tetranucleotide frequencies are the most commonly used alignment-free dissimilarity measures to detect HGT. By testing on simulated bacterial sequences and real data sets with known horizontal transferred genomic regions, we found that more advanced alignment-free dissimilarity measures such as CVTree and [Formula: see text] that take into account the background Markov sequences can solve HGT detection problems with significantly improved performance...
2018: Frontiers in Microbiology
Bih-Cheng Chen, Meng-Yu Hung, Hsueh-Fang Wang, Li-Jen Yeh, Sudhir Pandey, Ray-Jade Chen, Ruey-Lin Chang, Vijaya Padma Viswanadha, Kuan-Ho Lin, Chih-Yang Huang
Cardiomyocyte apoptosis is the major risk factor for the development of heart failure (HF). The purpose of this study was to evaluate the effects of Gamma-aminobutyric acid (GABA) tea on hypertension-induced cardiac apoptotic pathways in spontaneously hypertensive rats (SHR). In order to reveal the mechanisms, 36 male SHR at eight weeks of age, 200 g were divided into six groups. One group was fed water as a control group. Other rats were administered one of the following treatments: GABA tea at dose 150 and 300 mg/kg/day as low GABA tea (LGT) and high GABA tea (HGT) groups, respectively, pure GABA at dose 150 and 300 mg/kg/day as LG and HG groups, respectively, green tea (GT) as control of LGT and HGT groups...
April 30, 2018: Environmental Toxicology
James S Godde, Shakuntala Baichoo, Zahra Mungloo-Dilmohamud, Yasmina Jaufeerally-Fakim
A number of examples of putative eukaryote-to-prokaryote horizontal gene transfer (HGT) have been proposed in the past using phylogenetic analysis in support of these claims but none have attempted to map these gene transfers to the presence of genomic islands (GIs) in the host. Two of these cases have been examined in detail, including an ATP sulfurylase (ATPS) gene and a class I fructose bisphosphate aldolase (FBA I) gene that were putatively transferred to cyanobacteria of the genus Prochlorococcus from either green or red algae, respectively...
June 2018: Microbiological Research
F R Savory, D S Milner, D C Miles, T A Richards
Horizontal gene transfer (HGT) can equip organisms with novel genes, expanding the repertoire of genetic material available for evolutionary innovation and allowing recipient lineages to colonise new environments. However, few studies have characterised the functions of HGT genes experimentally or examined post-acquisition functional divergence. Here we report the use of ancestral sequence reconstruction and heterologous expression in Saccharomyces cerevisiae to examine the evolutionary history of an oomycete transporter gene family that was horizontally acquired from fungi...
April 25, 2018: Molecular Biology and Evolution
Raffael C Inglin, Leo Meile, Marc J A Stevens
BACKGROUND: Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes are largely ignored in taxonomy. The genus Lactobacillus consists of 173 species and many genomes are available to study taxonomy and evolutionary events. RESULTS: We analyzed and clustered 98 completely sequenced genomes of the genus Lactobacillus and 234 draft genomes of 5 different Lactobacillus species, i...
April 24, 2018: BMC Genomics
Tu Anh Nguyen, Jamie Greig, Asif Khan, Cara Goh, Gregory Jedd
Horizontal gene transfer (HGT) can promote evolutionary adaptation by transforming a species' relationship to the environment. In most well-understood cases of HGT, acquired and donor functions appear to remain closely related. Thus, the degree to which HGT can lead to evolutionary novelties remains unclear. Mucorales fungi sense gravity through the sedimentation of vacuolar protein crystals. Here, we identify the octahedral crystal matrix protein (OCTIN). Phylogenetic analysis strongly supports acquisition of octin by HGT from bacteria...
April 2018: PLoS Biology
Todd A Gray, Keith M Derbyshire
This review discusses a novel form of horizontal gene transfer (HGT) found in mycobacteria called Distributive Conjugal Transfer (DCT). While satisfying the criteria for conjugation, DCT occurs by a mechanism so distinct from oriT-mediated conjugation that it could be considered a fourth category of HGT. DCT involves the transfer of chromosomal DNA between mycobacteria and, most significantly, generates transconjugants with mosaic genomes of the parental strains. Multiple segments of donor chromosomal DNA can be co-transferred regardless of their location or the genetic selection and, as a result, the transconjugant genome contains many donor-derived segments; hence the name DCT...
April 18, 2018: Molecular Microbiology
Ximin Zeng, Jun Lin
Antibiotic resistance (AR) is ancient. Use of antibiotics is a selective driving force that enriches AR genes and promotes the emergence of resistant pathogens. It also has been widely accepted that horizontal gene transfer (HGT) occurs everywhere and plays a critical role in the transmission of AR genes among bacteria. However, our understanding of HGT processes primarily build on extensive in vitro studies; to date, there is still a significant knowledge gap regarding in situ HGT events as well as the factors that influence HGT in different ecological niches...
December 2017: Animal Health Research Reviews
Muhammet Zopun, Kathrin I Liszt, Verena Stoeger, Maik Behrens, Ulrike Redel, Jakob P Ley, Joachim Hans, Veronika Somoza
The non-caloric sweeteners (NCS) cyclamate (Cycl) and acesulfame K (AceK) are widely added to foods and beverages. Little is known about their impact on gastric acid secretion (GAS), which is stimulated by dietary protein and bitter-tasting compounds. Since Cycl and AceK have a bitter off-taste in addition to their sweet-taste, we hypothesized they modulate mechanisms of GAS in human gastric parietal cells (HGT-1). HGT-1 cells were exposed to sweet tastants (50 mM of glucose, D-threonine, Cycl or AceK), and analyzed for their intracellular pH index (IPX), as indicator of proton secretion by means of a pH-sensitive dye, and for mRNA-levels of GAS-associated genes by RT-qPCR...
April 17, 2018: Journal of Agricultural and Food Chemistry
Andrea Di Cesare, Pedro J Cabello-Yeves, Nathan A M Chrismas, Patricia Sánchez-Baracaldo, Michaela M Salcher, Cristiana Callieri
BACKGROUND: Many cyanobacteria are capable of fixing atmospheric nitrogen, playing a crucial role in biogeochemical cycling. Little is known about freshwater unicellular cyanobacteria Synechococcus spp. at the genomic level, despite being recognised of considerable ecological importance in aquatic ecosystems. So far, it has not been shown whether these unicellular picocyanobacteria have the potential for nitrogen fixation. Here, we present the draft-genome of the new pink-pigmented Synechococcus-like strain Vulcanococcus limneticus...
April 16, 2018: BMC Genomics
Ning Zhang, Guohong Cai, Dana C Price, Jo Anne Crouch, Pierre Gladieux, Bradley Hillman, Chang Hyun Khang, Marc-Henri LeBrun, Yong-Hwan Lee, Jing Luo, Huan Qiu, Daniel Veltri, Jennifer H Wisecaver, Jie Zhu, Debashish Bhattacharya
The rice blast fungus Pyricularia oryzae (syn. Magnaporthe oryzae, Magnaporthe grisea), a member of the order Magnaporthales in the class Sordariomycetes, is an important plant pathogen and a model species for studying pathogen infection and plant-fungal interaction. In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis...
April 12, 2018: Scientific Reports
C Citti, E Dordet-Frisoni, L X Nouvel, C H Kuo, E Baranowski
The class Mollicutes (trivial name "mycoplasma") is composed of wall-less bacteria with reduced genomes whose evolution was long thought to be only driven by gene losses. Recent evidences of massive horizontal gene transfer (HGT) within and across species provided a new frame to understand the successful adaptation of these minimal bacteria to a broad range of hosts. Mobile genetic elements are being identified in a growing number of mycoplasma species, but integrative and conjugative elements (ICEs) are emerging as pivotal in HGT...
April 12, 2018: Current Issues in Molecular Biology
Alba Blesa, Beate Averhoff, José Berenguer
The small amount of genetic content in thermophiles generally limits their adaptability to environmental changes. In Thermus spp., very active horizontal gene transfer (HGT) mechanisms allow the rapid spread of strain-specific adaptive gene modules among the entire population. Constitutive expression of a rather particular and highly efficient DNA transport apparatus (DTA) is at the center of this HGT-mediated enhanced adaptability. The function of the DTA is dependent on the integrity and longevity of the extracellular DNA (eDNA) being transformed, which can be improved by the production of extracellular vesicles (EV) through lysis of a fraction of the population...
April 12, 2018: Current Issues in Molecular Biology
Carla Gonçalves, Jennifer H Wisecaver, Jacek Kominek, Madalena Salema Oom, Maria José Leandro, Xing-Xing Shen, Dana A Opulente, Xiaofan Zhou, David Peris, Cletus P Kurtzman, Chris Todd Hittinger, Antonis Rokas, Paula Gonçalves
Fructophily is a rare trait that consists of the preference for fructose over other carbon sources. Here, we show that in a yeast lineage (the Wickerhamiella / Starmerella , W/S clade) comprised of fructophilic species thriving in the high-sugar floral niche, the acquisition of fructophily is concurrent with a wider remodeling of central carbon metabolism. Coupling comparative genomics with biochemical and genetic approaches, we gathered ample evidence for the loss of alcoholic fermentation in an ancestor of the W/S clade and subsequent reinstatement through either horizontal acquisition of homologous bacterial genes or modification of a pre-existing yeast gene...
April 12, 2018: ELife
A B Westbye, L Kater, C Wiesmann, H Ding, C K Yip, J T Beatty
Several members of the Rhodobacterales ( Alphaproteobacteria ) produce a conserved horizontal gene transfer vector, called gene transfer agent (GTA), that appears to have evolved from a bacteriophage. The model system to study GTA biology is the R. capsulatus GTA (RcGTA), a small, tailed bacteriophage-like particle produced by a subset of the cells in a culture. The response regulator CtrA is conserved in the Alphaproteobacteria and is an essential regulator of RcGTA production: it controls production and maturation of the RcGTA particle and RcGTA release from cells...
April 6, 2018: Applied and Environmental Microbiology
Hyaekang Kim, Woori Kwak, Sook Hee Yoon, Dae-Kyung Kang, Heebal Kim
Recent comparative genomics studies have suggested that horizontal gene transfer (HGT) is one of the major processes in bacterial evolution. In this study, HGT events of 64 Chlamydia strains were investigated based on the pipeline employed in HGTree database constructed in our recent study. Tree reconciliation method was applied in order to calculate feasible HGT events. Following initial detection and an evaluation procedure, evidence of the HGT was identified in 548 gene families including 42 gene families transferred from outside of Chlamydiae phylum with high reliability...
2018: PloS One
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