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horizontal gene transfers

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https://www.readbyqxmd.com/read/29143727/characterization-of-clinically-isolated-thymidine-dependent-small-colony-variants-of-escherichia-coli-producing-extended-spectrum-%C3%AE-lactamase
#1
Tatsuya Negishi, Takehisa Matsumoto, Kazuki Horiuchi, Eriko Kasuga, Tatsuya Natori, Mina Matsuoka, Naoko Ogiwara, Mitsutoshi Sugano, Takeshi Uehara, Noriyuki Nagano, Takayuki Honda
PURPOSE: Thymidine-dependent small-colony variants (TD-SCVs) are difficult to detect or test for antimicrobial susceptibility. We investigated the characteristics of clonal TD-SCVs of Escherichia coli, both with and without blaCTX-M-3, isolated from a patient. METHODOLOGY: Mutation in the thyA gene was analysed by sequencing, and morphological abnormalities in the colonies and cells of the isolates were examined. Additionally, conjugational transfer experiments were performed to prove the horizontal transferability of plasmids harbouring resistance genes...
November 16, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29143083/the-polyphyletic-origins-of-primase-helicase-bifunctional-proteins
#2
Ankita Gupta, Supriya Patil, Ramya Vijayakumar, Kiran Kondabagil
We studied the evolutionary relationships of different primase-helicase bifunctional proteins, found mostly in viruses, virophages, plasmids, and organellar genomes, by phylogeny and correlation analysis. Our study suggests independent origins of primase-helicase bifunctional proteins resulting from multiple fusion events between genes encoding primase and helicase domains of different families. The correlation analysis further indicated strong functional dependencies of domains in the bifunctional proteins that are part of smaller genomes and plasmids...
November 15, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29138003/serine-threonine-protein-kinases-from-bacteria-archaea-and-eukarya-share-a-common-evolutionary-origin-deeply-rooted-in-the-tree-of-life
#3
Ivan Andreas Stancik, Martin Sebastijan Šestak, Boyang Ji, Marina Axelson-Fisk, Damjan Franjevic, Carsten Jers, Tomislav Domazet-Lošo, Ivan Mijakovic
The main family of serine/threonine/tyrosine protein kinases present in eukarya was defined and described by Hanks et al. in 1988. It was initially believed that these kinases do not exist in bacteria, but extensive genome sequencing revealed their existence in many bacteria. For historical reasons, the term "eukaryotic-type kinases" propagated in the literature to describe bacterial members of this protein family. Here, we argue that this term should be abandoned as a misnomer, and we provide several lines of evidence to support this claim...
November 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29137267/tumacrophage-macrophages-transformed-into-tumor-stem-like-cells-by-virulent-genetic-material-from-tumor-cells
#4
Yizhuang Zhang, Na Zhou, Xiuyan Yu, Xuehui Zhang, Shanxin Li, Zhen Lei, Ruobi Hu, Hui Li, Yiqing Mao, Xi Wang, Jinshu Zhang, Yuan Li, Hongyan Guo, David M Irwin, Gang Niu, Huanran Tan
Tumor-associated macrophages are regarded as tumor-enhancers as they have key roles in the subversion of adaptive immunity and in inflammatory circuits that promote tumor progression. Here, we show that cancer cells can subvert macrophages yielding cells that have gained pro-tumor functions. When macrophages isolated from mice or humans are co-cultured with dead cancer cell line cells, induced to undergo apoptosis to mimic chemotherapy, up-regulation of pro-tumor gene expression was identified. Phagocytosis of apoptotic cancer cells by macrophages resulted in their transformation into tumor stem (initiating)-like cells, as indicated by the expression of epithelial markers (e...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29134153/hgtsim-a-simulator-for-horizontal-gene-transfer-hgt-in-microbial-communities
#5
Weizhi Song, Kerrin Steensen, Torsten Thomas
The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce defined HGT within a microbial community. Here, we present HgtSIM, a pipeline to simulate HGT event among microbial community members with user-defined mutation levels. It was developed for testing and benchmarking pipelines for recovering HGTs from complex microbial datasets...
2017: PeerJ
https://www.readbyqxmd.com/read/29133838/fungal-networks-serve-as-novel-ecological-routes-for-enrichment-and-dissemination-of-antibiotic-resistance-genes-as-exhibited-by-microcosm-experiments
#6
Rashid Nazir, Ju-Pei Shen, Jun-Tao Wang, Hang-Wei Hu, Ji-Zheng He
Antibiotic resistance genes (ARGs) in the environment and their subsequent acquisition by clinically important microorganisms are a serious concern. However, the spread of environmental ARGs remain largely unknown. We report, for the first time, the involvement of soil fungi in the distribution of bacteria with ARGs via soil microcosms. qPCR assay detected unique ARGs specifically found in the mycosphere of different fungi. Interestingly, the taxonomically and ecologically different fungi exerted different selection pressures on ARGs originating from the same source...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133277/orthognc-a-software-for-accurate-identification-of-orthologs-based-on-gene-neighborhood-conservation
#7
Soheil Jahangiri-Tazehkand, Limsoon Wong, Changiz Eslahchi
Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood information can be used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software for accurately predicting pairwise orthology relations based on gene neighborhood conservation...
November 10, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29127343/global-phylogenetic-analysis-of-escherichia-coli-and-plasmids-carrying-the-mcr-1-gene-indicates-bacterial-diversity-but-plasmid-restriction
#8
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
https://www.readbyqxmd.com/read/29126189/comparative-genome-analysis-reveals-adaptation-to-the-ectophytic-lifestyle-of-sooty-blotch-and-flyspeck-fungi
#9
Chao Xu, Rong Zhang, Guangyu Sun, Mark L Gleason
Sooty blotch and flyspeck (SBFS) fungi are a distinctive group of plant pathogens which, although phylogenetically diverse, occupy an exclusively surface-dwelling niche. They cause economic losses by superficially blemishing the fruit of several tree crops, principally apple, in moist temperate regions worldwide. In this study, we performed genome-wide comparative analyses separately within three pairs of species of ascomycete pathogens; each pair contained an SBFS species as well as a closely related but plant-penetrating parasite (PPP) species...
November 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29125597/phage-mobility-is-a-core-determinant-of-phage-bacteria-coexistence-in-biofilms
#10
Matthew Simmons, Knut Drescher, Carey D Nadell, Vanni Bucci
Many bacteria are adapted for attaching to surfaces and for building complex communities, termed biofilms. The biofilm mode of life is predominant in bacterial ecology. So too is the exposure of bacteria to ubiquitous viral pathogens, termed bacteriophages. Although biofilm-phage encounters are likely to be common in nature, little is known about how phages might interact with biofilm-dwelling bacteria. It is also unclear how the ecological dynamics of phages and their hosts depend on the biological and physical properties of the biofilm environment...
November 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/29122240/geosmin-production-and-polyphasic-characterization-of-oscillatoria-limosa-agardh-ex-gomont-isolated-from-the-open-canal-of-a-large-drinking-water-system-in-tianjin-city-china
#11
Fangfang Cai, Gongliang Yu, Kai Zhang, Youxin Chen, Qiang Li, Yiming Yang, Jinlin Xie, Yilang Wang, Renhui Li
Taste and odor (T & O) episodes always cause strong effects on drinking water supply system. Luanhe River diversion into Tianjin City in China is an important drinking water resource. Massive growth of a benthic filamentous cyanobacterium with geosmin production in the open canal caused a strong earthy odor episode in Tianjin. On the basis of the morphological and molecular identification of this cyanobacterium as Oscillatoria limosa Agardh ex Gomont, the genetic basis for geosmin biosynthesis and factors influencing growth and geosmin production of O...
November 2017: Harmful Algae
https://www.readbyqxmd.com/read/29120392/impact-of-lateral-transfers-on-the-genomes-of-lepidoptera
#12
REVIEW
Jean-Michel Drezen, Thibaut Josse, Annie Bézier, Jérémy Gauthier, Elisabeth Huguet, Elisabeth Anne Herniou
Transfer of DNA sequences between species regardless of their evolutionary distance is very common in bacteria, but evidence that horizontal gene transfer (HGT) also occurs in multicellular organisms has been accumulating in the past few years. The actual extent of this phenomenon is underestimated due to frequent sequence filtering of "alien" DNA before genome assembly. However, recent studies based on genome sequencing have revealed, and experimentally verified, the presence of foreign DNA sequences in the genetic material of several species of Lepidoptera...
November 9, 2017: Genes
https://www.readbyqxmd.com/read/29120256/silent-but-deadly-is200-promotes-pathogenicity-in-salmonella-typhimurium
#13
Michael J Ellis, Lindsey A Carfrae, Craig R Macnair, Ryan S Trussler, Eric D Brown, David B Haniford
Bacterial transposons were long thought of as selfish mobile genetic elements that propagate at the expense of 'host' bacterium fitness. However, limited transposition can benefit the host organism by promoting DNA rearrangements and facilitating horizontal gene transfer. Here we discuss and provide context for our recently published work which reported the surprising finding that an otherwise dormant transposon, IS200, encodes a regulatory RNA in Salmonella Typhimurium. This previous work identified a trans-acting sRNA that is encoded in the 5'UTR of IS200 transposase mRNA (tnpA)...
November 9, 2017: RNA Biology
https://www.readbyqxmd.com/read/29117219/cellular-and-exosome-mediated-molecular-defense-mechanism-in-bovine-granulosa-cells-exposed-to-oxidative-stress
#14
Mohammed Saeed-Zidane, Lea Linden, Dessie Salilew-Wondim, Eva Held, Christiane Neuhoff, Ernst Tholen, Michael Hoelker, Karl Schellander, Dawit Tesfaye
Various environmental insults including diseases, heat and oxidative stress could lead to abnormal growth, functions and apoptosis in granulosa cells during ovarian follicle growth and oocyte maturation. Despite the fact that cells exposed to oxidative stress are responding transcriptionally, the potential release of transcripts associated with oxidative stress response into extracellular space through exosomes is not yet determined. Therefore, here we aimed to investigate the effect of oxidative stress in bovine granulosa cells in vitro on the cellular and exosome mediated defense mechanisms...
2017: PloS One
https://www.readbyqxmd.com/read/29116639/dna-replication-fidelity-in-the-mycobacterium-tuberculosis-complex
#15
Digby F Warner, Jeremy M Rock, Sarah M Fortune, Valerie Mizrahi
Mycobacterium tuberculosis is genetically isolated, with no evidence for horizontal gene transfer or the acquisition of episomal genetic information in the modern evolution of strains of the Mycobacterium tuberculosis complex. When considered in the context of the specific features of the disease M. tuberculosis causes (e.g., transmission via cough aerosol, replication within professional phagocytes, subclinical persistence, and stimulation of a destructive immune pathology), this implies that to understand the mechanisms ensuring preservation of genomic integrity in infecting mycobacterial populations is to understand the source of genetic variation, including the emergence of microdiverse sub-populations that may be linked to the acquisition of drug resistance...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29112840/antibiotics-and-common-antibacterial-biocides-stimulate-horizontal-transfer-of-resistance-at-low-concentrations
#16
J Jutkina, N P Marathe, C-F Flach, D G J Larsson
There is a rising concern that antibiotics, and possibly other antimicrobial agents, can promote horizontal transfer of antibiotic resistance genes. For most types of antimicrobials their ability to induce conjugation below minimal inhibitory concentrations (MICs) is still unknown. Our aim was therefore to explore the potential of commonly used antibiotics and antibacterial biocides to induce horizontal transfer of antibiotic resistance. Effects of a wide range of sub-MIC concentrations of the antibiotics cefotaxime, ciprofloxacin, gentamicin, erythromycin, sulfamethoxazole, trimethoprim and the antibacterial biocides chlorhexidine digluconate, hexadecyltrimethylammoniumchloride and triclosan were investigated using a previously optimized culture-based assay with a complex bacterial community as a donor of mobile resistance elements and a traceable Escherichia coli strain as a recipient...
November 4, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29112720/fusiondb-assessing-microbial-diversity-and-environmental-preferences-via-functional-similarity-networks
#17
Zhu Chengsheng, Mahlich Yannick, Miller Maximilian, Bromberg Yana
Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across taxa. While microbial similarities are often reported in terms of taxonomic relationships, no existing databases directly link microbial functions to the environment. We previously developed a method for comparing microbial functional similarities on the basis of proteins translated from their sequenced genomes...
November 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29112165/poxvirus-host-range-genes-and-virus-host-spectrum-a-critical-review
#18
REVIEW
Graziele Pereira Oliveira, Rodrigo Araújo Lima Rodrigues, Maurício Teixeira Lima, Betânia Paiva Drumond, Jônatas Santos Abrahão
The Poxviridae family is comprised of double-stranded DNA viruses belonging to nucleocytoplasmic large DNA viruses (NCLDV). Among the NCLDV, poxviruses exhibit the widest known host range, which is likely observed because this viral family has been more heavily investigated. However, relative to each member of the Poxviridae family, the spectrum of the host is variable, where certain viruses can infect a large range of hosts, while others are restricted to only one host species. It has been suggested that the variability in host spectrum among poxviruses is linked with the presence or absence of some host range genes...
November 7, 2017: Viruses
https://www.readbyqxmd.com/read/29109705/complete-genome-sequence-of-vibrio-campbellii-lmb-29-isolated-from-red-drum-with-four-native-megaplasmids
#19
Jinxin Liu, Zhe Zhao, Yiqing Deng, Yan Shi, Yupeng Liu, Chao Wu, Peng Luo, Chaoqun Hu
Vibrio spp. are the most common pathogens for animals reared in aquaculture. Vibrio campbellii, which is often involved in shrimp, fish and mollusks diseases, is widely distributed in the marine environment worldwide, but our knowledge about its pathogenesis and antimicrobial resistance is very limited. The existence of this knowledge gap is at least partially because that V. campbellii was originally classified as Vibrio harveyi, and the detailed information of its comparative genome analysis to other Vibrio spp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29109702/genomic-comparison-among-lethal-invasive-strains-of-streptococcus-pyogenes-serotype-m1
#20
Gabriel R Fernandes, Aulus E A D Barbosa, Renan N Almeida, Fabíola F Dos S Castro, Marina de C P da Ponte, Celio Faria-Junior, Fernanda M P Müller, Antônio A B Viana, Dario Grattapaglia, Octavio L Franco, Sérgio A Alencar, Simoni C Dias
Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a human pathogen that causes diverse human diseases including streptococcal toxic shock syndrome (STSS). A GAS outbreak occurred in Brasilia, Brazil, during the second half of the year 2011, causing 26 deaths. Whole genome sequencing was performed using Illumina platform. The sequences were assembled and genes were predicted for comparative analysis with emm type 1 strains: MGAS5005 and M1 GAS. Genomics comparison revealed one of the invasive strains that differ from others isolates and from emm 1 reference genomes...
2017: Frontiers in Microbiology
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