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https://www.readbyqxmd.com/read/28737000/chemoprofile-and-functional-diversity-of-fungal-and-bacterial-endophytes-and-role-of-ecofactors-a-review
#1
REVIEW
Aiyatullah Shah, Qazi Parvaiz Hassan, Saleem Mushtaq, Aabid Manzoor Shah, Aehtesham Hussain
Endophytes represent a hidden world within plants. Almost all plants that are studied harbor one or more endophytes, which help their host to survive against pathogens and changing adverse environmental conditions. Fungal and bacterial endophytes with distinct ecological niches show important biological activities and ecological functions. Their unique physiological and biochemical characteristics lead to the production of niche specific secondary metabolites that may have pharmacological potential. Identification of specific secondary metabolites in adverse environment can also help us in understanding mechanisms of host tolerance against stress condition such as biological invasions, salt, drought, temperature...
July 24, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28732463/common-and-phylogenetically-widespread-coding-for-peptides-by-bacterial-small-rnas
#2
Robin C Friedman, Stefan Kalkhof, Olivia Doppelt-Azeroual, Stephan A Mueller, Martina Chovancová, Martin von Bergen, Benno Schwikowski
BACKGROUND: While eukaryotic noncoding RNAs have recently received intense scrutiny, it is becoming clear that bacterial transcription is at least as pervasive. Bacterial small RNAs and antisense RNAs (sRNAs) are often assumed to be noncoding, due to their lack of long open reading frames (ORFs). However, there are numerous examples of sRNAs encoding for small proteins, whether or not they also have a regulatory role at the RNA level. METHODS: Here, we apply flexible machine learning techniques based on sequence features and comparative genomics to quantify the prevalence of sRNA ORFs under natural selection to maintain protein-coding function in 14 phylogenetically diverse bacteria...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28729858/toxin-antitoxin-systems-in-estuarine-synechococcus-strain-cb0101-and-their-transcriptomic-responses-to-environmental-stressors
#3
David Marsan, Allen Place, Daniel Fucich, Feng Chen
Bacterial toxin-antitoxin (TA) systems are genetic elements composed of a toxin gene and its cognate antitoxin, with the ability to regulate growth. TA systems have not previously been reported in marine Synechococcus or Prochlorococcus. Here we report the finding of seven TA system pairs (Type II) in the estuarine Synechococcus CB0101, and their responses of these TA genes to under different stress conditions, which include; nitrogen and phosphate starvation, phage infection, zinc toxicity, and photo-oxidation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28726719/sima-cells-for-a-serotype-specific-and-sensitive-cell-based-neutralization-test-for-botulinum-toxin-a-and-e
#4
Nicola Bak, Shalini Rajagopal, Paul Stickings, Dorothea Sesardic
Botulinum toxins (BoNTs), of which there are seven serotypes, are among the most potent neurotoxins, with serotypes A, B and E causing human botulism. Antitoxins form the first line of treatment for botulism, and functional, highly sensitive in vitro methods for toxin neutralization are needed to replace the current in vivo methods used for determination of antitoxin potency. In this preliminary proof of concept study, we report the development of a neutralization test using the neuroblastoma SiMa cell line...
July 20, 2017: Toxins
https://www.readbyqxmd.com/read/28724903/co-expression-network-analysis-of-toxin-antitoxin-loci-in-mycobacterium-tuberculosis-reveals-key-modulators-of-cellular-stress
#5
Amita Gupta, Balaji Venkataraman, Madavan Vasudevan, Kiran Gopinath Bankar
Research on toxin-antitoxin loci (TA loci) is gaining impetus due to their ubiquitous presence in bacterial genomes and their observed roles in stress survival, persistence and drug tolerance. The present study investigates the expression profile of all the seventy-nine TA loci found in Mycobacterium tuberculosis. The bacterium was subjected to multiple stress conditions to identify key players of cellular stress response and elucidate a TA-coexpression network. This study provides direct experimental evidence for transcriptional activation of each of the seventy-nine TA loci following mycobacterial exposure to growth-limiting environments clearly establishing TA loci as stress-responsive modules in M...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28705271/molecular-and-epidemiological-characterization-of-infant-botulism-in-beijing-china
#6
Yin Ping Dong, Wei Wang, Tao Jiang, Jin Xu, Chun Hui Han, Shao Fei Yan, Séamus Fanning, Ying Li, Xiao Chen Ma, Di Zhang, Yao Zhao, Biao Zeng, Feng Qin Li
Laboratory-based pathogen isolation, identification, and toxicity determination were performed on samples from a suspected case of infant botulism. Mice injected with cultures generated from the enema sample and ingested Powered infant formula (PIF) presented typical signs of botulism. Antitoxins to polyvalent botulinum neurotoxins (BoNTs) and monovalent BoNT type B antitoxin had protective effects. Clostridium botulinum isolated from the enema and residual PIF samples were positive for type B toxin. Pulsed-field gel electrophoresis (PFGE) revealed that the two strains of C...
June 2017: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/28700055/biological-and-molecular-properties-of-yellow-venom-of-the-amazonian-coral-snake-micrurus-surinamensis
#7
Fabiana da Rocha Oliveira, Maria das Dores Nogueira Noronha, Jorge Luis Lopez Lozano
INTRODUCTION: The coral snake Micrurus surinamensis, which is widely distributed throughout Amazonia, has a neurotoxic venom. It is important to characterize the biological and molecular properties of this venom in order to develop effective antitoxins. METHODS: Toxins from the venom of M. surinamensis were analyzed by two-dimensional polyacrylamide gel electrophoresis and their neurotoxic effects in vivo were evaluated. RESULTS AND CONCLUSIONS: Most proteins in the venom had masses < 14kDa, low phospholipase A2 activity, and no proteolytic activity...
May 2017: Revista da Sociedade Brasileira de Medicina Tropical
https://www.readbyqxmd.com/read/28696422/metagenomic-binning-of-a-marine-sponge-microbiome-reveals-unity-in-defense-but-metabolic-specialization
#8
Beate M Slaby, Thomas Hackl, Hannes Horn, Kristina Bayer, Ute Hentschel
Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes involved in host colonization and extracellular matrix utilization in sponge symbionts...
July 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28691660/endoribonuclease-type-ii-toxin-antitoxin-systems-functional-or-selfish
#9
Bhaskar Chandra Mohan Ramisetty, Ramachandran Sarojini Santhosh
Most bacterial genomes have multiple type II toxin-antitoxin systems (TAs) that encode two proteins which are referred to as a toxin and an antitoxin. Toxins inhibit a cellular process, while the interaction of the antitoxin with the toxin attenuates the toxin's activity. Endoribonuclease-encoding TAs cleave RNA in a sequence-dependent fashion, resulting in translational inhibition. To account for their prevalence and retention by bacterial genomes, TAs are credited with clinically significant phenomena, such as bacterial programmed cell death, persistence, biofilms and anti-addiction to plasmids...
July 8, 2017: Microbiology
https://www.readbyqxmd.com/read/28690609/diversity-prevalence-and-longitudinal-occurrence-of-type-ii-toxin-antitoxin-systems-of-pseudomonas-aeruginosa-infecting-cystic-fibrosis-lungs
#10
Sandra B Andersen, Melanie Ghoul, Ashleigh S Griffin, Bent Petersen, Helle K Johansen, Søren Molin
Type II toxin-antitoxin (TA) systems are most commonly composed of two genes encoding a stable toxin, which harms the cell, and an unstable antitoxin that can inactivate it. TA systems were initially characterized as selfish elements, but have recently gained attention for regulating general stress responses responsible for pathogen virulence, formation of drug-tolerant persister cells and biofilms-all implicated in causing recalcitrant chronic infections. We use a bioinformatics approach to explore the distribution and evolution of type II TA loci of the opportunistic pathogen, Pseudomonas aeruginosa, across longitudinally sampled isolates from cystic fibrosis lungs...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28690594/toxin-%C3%AE-triggers-a-survival-response-to-cope-with-stress-and-persistence
#11
María Moreno-Del Álamo, Mariangela Tabone, Virginia S Lioy, Juan C Alonso
Bacteria have evolved complex regulatory controls in response to various environmental stresses. Protein toxins of the ζ superfamily, found in prominent human pathogens, are broadly distributed in nature. We show that ζ is a uridine diphosphate-N-acetylglucosamine (UNAG)-dependent ATPase whose activity is inhibited in vitro by stoichiometric concentrations of ε2 antitoxin. In vivo, transient ζ expression promotes a reversible multi-level response by altering the pool of signaling purine nucleotides, which leads to growth arrest (dormancy), although a small cell subpopulation persists rather than tolerating toxin action...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28687759/emerging-patterns-of-plasmid-host-coevolution-that-stabilize-antibiotic-resistance
#12
Thibault Stalder, Linda M Rogers, Chris Renfrow, Hirokazu Yano, Zachary Smith, Eva M Top
Multidrug resistant bacterial pathogens have become a serious global human health threat, and conjugative plasmids are important drivers of the rapid spread of resistance to last-resort antibiotics. Whereas antibiotics have been shown to select for adaptation of resistance plasmids to their new bacterial hosts, or vice versa, a general evolutionary mechanism has not yet emerged. Here we conducted an experimental evolution study aimed at determining general patterns of plasmid-bacteria evolution. Specifically, we found that a large conjugative resistance plasmid follows the same evolutionary trajectories as its non-conjugative mini-replicon in the same and other species...
July 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28677629/mechanisms-for-differential-protein-production-in-toxin-antitoxin-systems
#13
Heather S Deter, Roderick V Jensen, William H Mather, Nicholas C Butzin
Toxin-antitoxin (TA) systems are key regulators of bacterial persistence, a multidrug-tolerant state found in bacterial species that is a major contributing factor to the growing human health crisis of antibiotic resistance. Type II TA systems consist of two proteins, a toxin and an antitoxin; the toxin is neutralized when they form a complex. The ratio of antitoxin to toxin is significantly greater than 1.0 in the susceptible population (non-persister state), but this ratio is expected to become smaller during persistence...
July 4, 2017: Toxins
https://www.readbyqxmd.com/read/28676719/srna-and-cis-antisense-srna-identification-in-staphylococcus-aureus-highlights-an-unusual-srna-gene-cluster-with-one-encoding-a-secreted-peptide
#14
Julie Bronsard, Gaetan Pascreau, Mohamed Sassi, Tony Mauro, Yoann Augagneur, Brice Felden
The human pathogen Staphylococcus aureus expresses a set of transcriptional factors and small RNAs (sRNAs) to adapt to environmental variations. Recent harmonization of staphylococcal sRNA data allowed us to search for novel sRNAs using DETR'PROK, a computational pipeline for identifying sRNA in prokaryotes. We performed RNA-Seq on Newman strain and identified a set of 48 sRNA candidates. To avoid bioinformatic artefacts, we applied a series of cut-offs and tested experimentally each selected intergenic region...
July 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28675659/characterization-of-a-deinococcus-radiodurans-mazf-a-uaca-specific-rna-endoribonuclease
#15
Tatsuki Miyamoto, Yuri Ota, Akiko Yokota, Tetsushi Suyama, Satoshi Tsuneda, Naohiro Noda
Microbes are known to withstand environmental stresses by using chromosomal toxin-antitoxin systems. MazEF is one of the most extensively studied toxin-antitoxin systems. In stressful environments, MazF toxins modulate translation by cleaving single-stranded RNAs in a sequence-specific fashion. Previously, a chromosomal gene located at DR0417 in Deinococcus radiodurans was predicted to code for a MazF endoribonuclease (MazFDR0417 ); however, its function remains unclear. In the present study, we characterized the molecular function of MazFDR0417 ...
July 3, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28674066/contribution-of-the-chromosomal-ccdab-operon-to-bacterial-drug-tolerance
#16
Kritika Gupta, Arti Tripathi, Alishan Sahu, Raghavan Varadarajan
One of the first identified and best studied toxin-antitoxin systems in Escherichia coli is the F-plasmid based CcdAB system. This system is involved in plasmid maintenance through post-segregational killing. More recently, ccdAB homologs have been found on the chromosome, including in pathogenic strains of E. coli and other bacteria. However the functional role of chromosomal ccdAB genes, if any, has remained unclear. We show that both the native ccd operon of the E.coliO157 strain, as well as the ccd operon from the F- plasmid, when inserted on the E...
July 3, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28669616/clostridium-difficile-chimeric-toxin-receptor-binding-domain-vaccine-induced-protection-against-different-strains-in-active-and-passive-challenge-models
#17
Jing-Hui Tian, Gregory Glenn, David Flyer, Bin Zhou, Ye Liu, Eddie Sullivan, Hua Wu, James F Cummings, Larry Elllingsworth, Gale Smith
Clostridium difficile is the number one cause of nosocomial antibiotic-associated diarrhea in developed countries. Historically, pathogenesis was attributed two homologous glucosylating toxins, toxin-A (TcdA) and toxin-B (TcdB). Over the past decade, however, highly virulent epidemic strains of C. difficile (B1/NAP1/027) have emerged and are linked to an increase in morbidity and mortality. Increased virulence is attributed to multiple factors including: increased production of A- and B-toxins; production of binary toxin (CDT); and the emergence of more toxic TcdB variants (TcdB(027))...
July 24, 2017: Vaccine
https://www.readbyqxmd.com/read/28652353/disentangling-the-effects-of-selection-and-loss-bias-on-gene-dynamics
#18
Jaime Iranzo, José A Cuesta, Susanna Manrubia, Mikhail I Katsnelson, Eugene V Koonin
We combine mathematical modeling of genome evolution with comparative analysis of prokaryotic genomes to estimate the relative contributions of selection and intrinsic loss bias to the evolution of different functional classes of genes and mobile genetic elements (MGE). An exact solution for the dynamics of gene family size was obtained under a linear duplication-transfer-loss model with selection. With the exception of genes involved in information processing, particularly translation, which are maintained by strong selection, the average selection coefficient for most nonparasitic genes is low albeit positive, compatible with observed positive correlation between genome size and effective population size...
July 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28637172/identification-of-four-type-ii-toxin-antitoxin-systems-in-actinobacillus-pleuropneumoniae
#19
Chengkun Zheng, Xigong Zhao, Ting Zeng, Manman Cao, Jiali Xu, Guolin Shi, Jinquan Li, Huanchun Chen, Weicheng Bei
Toxin-antitoxin systems are small genetic elements that are widely prevalent in the genomes of bacteria and archaea. These modules have been identified in various bacteria and proposed to play an important role in bacterial physiology and virulence. However, their presence in the genomes of Actinobacillus species has received no attention. In this study, we describe the identification of four type II TA systems in Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia. Reverse transcription PCR analysis revealed that the genes encoding the toxin and antitoxin are co-transcribed...
June 20, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28621109/comparative-genomic-analysis-of-lactobacillus-plantarum-gb-lp1-isolated-from-traditional-korean-fermented-food
#20
Jihyun Yu, Sojin Ahn, Kwondo Kim, Kelsey Caetano-Anolles, Chanho Lee, Jungsun Kang, Kyungjin Cho, SookHee Yoon, Dae-Kyung Kang, Heebal Kim
As probiotics play an important role in maintaining a healthy gut flora environment through antitoxin activity and inhibition of pathogen colonization, they have been of interest to the medical research community for quite some time now. Probiotic bacteria such as Lactobacillus plantarum, which can be found in fermented food, are of particular interest given their easy accessibility. We performed whole genome sequencing and genomic analysis on a GB-LP1 strain of L. plantarum isolated from Korean traditional fermented food; this strain is well known for its functions in immune response, suppression of pathogen growth and anti-toxin effects...
June 16, 2017: Journal of Microbiology and Biotechnology
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