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Bacterial genomics

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https://www.readbyqxmd.com/read/28804480/microbial-community-structure-and-the-persistence-of-cyanobacterial-populations-in-salt-crusts-of-the-hyperarid-atacama-desert-from-genome-resolved-metagenomics
#1
Kari M Finstad, Alexander J Probst, Brian C Thomas, Gary L Andersen, Cecilia Demergasso, Alex Echeverría, Ronald G Amundson, Jillian F Banfield
Although once thought to be devoid of biology, recent studies have identified salt deposits as oases for life in the hyperarid Atacama Desert. To examine spatial patterns of microbial species and key nutrient sources, we genomically characterized 26 salt crusts from three sites along a fog gradient. The communities are dominated by a large variety of Halobacteriales and Bacteroidetes, plus a few algal and Cyanobacterial species. CRISPR locus analysis suggests the distribution of a single Cyanobacterial population among all sites...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28802046/replication-transcription-conflicts-generate-r-loops-that-orchestrate-bacterial-stress-survival-and-pathogenesis
#2
Kevin S Lang, Ashley N Hall, Christopher N Merrikh, Mark Ragheb, Hannah Tabakh, Alex J Pollock, Joshua J Woodward, Julia E Dreifus, Houra Merrikh
Replication-transcription collisions shape genomes, influence evolution, and promote genetic diseases. Although unclear why, head-on transcription (lagging strand genes) is especially disruptive to replication and promotes genomic instability. Here, we find that head-on collisions promote R-loop formation in Bacillus subtilis. We show that pervasive R-loop formation at head-on collision regions completely blocks replication, elevates mutagenesis, and inhibits gene expression. Accordingly, the activity of the R-loop processing enzyme RNase HIII at collision regions is crucial for stress survival in B...
August 10, 2017: Cell
https://www.readbyqxmd.com/read/28802023/the-agrobacterium-vire2-effector-interacts-with-multiple-members-of-the-arabidopsis-vip1-protein-family
#3
Luyao Wang, Benoît Lacroix, Jianhua Guo, Vitaly Citovsky
T-DNA transfer from Agrobacterium to its host plant genome relies on multiple interactions between plant proteins and bacterial effectors. One of such plant proteins is the Arabidopsis VirE2 interacting protein (AtVIP1), a transcription factor that binds A. tumefaciens C58 VirE2, potentially acting as an adaptor between VirE2 and several other host factors. It remains unknown, however, whether the same VirE2 protein has evolved to interact with multiple VIP1 homologs in the same host, and whether VirE2 homologs encoded by different bacterial strains/species recognize AtVIP1 or its homologs...
August 12, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28801673/photosensitizer-in-lipid-nanoparticle-a-nano-scaled-approach-to-antibacterial-function
#4
Bishakh Rout, Chi-Hsien Liu, Wei-Chi Wu
Photosensitization-based antimicrobial therapy (PAT) is an alternative therapy aimed at achieving bacterial inactivation. Researchers use various photosensitizers to achieve bacterial inactivation. However, the most widely used approach involves the use of photosensitizers dispersed in aqueous solution, which could limit the effectiveness of photodynamic inactivation. Therefore, the approaches to encapsulate the photosensitizer in appropriate vehicles can enhance the delivery of the photosensitizer. Herein, Toluidine Blue O (TBO) was the photosensitizer, and lipid nanoparticles were used for its encapsulation...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801647/reconstruction-of-a-genome-scale-metabolic-network-of-komagataeibacter-nataicola-rzs01-for-cellulose-production
#5
Heng Zhang, Chao Ye, Nan Xu, Chuntao Chen, Xiao Chen, Fanshu Yuan, Yunhua Xu, Jiazhi Yang, Dongping Sun
Bacterial cellulose (BC) is widely used in industries owing to its high purity and strength. Although Komagataeibacter nataicola is a representative species for BC production, its intracellular metabolism leading to BC secretion is unclear. In the present study, a genome-scale metabolic network of cellulose-producing K. nataicola strain RZS01 was reconstructed to understand its metabolic behavior. This model iHZ771 comprised 771 genes, 2035 metabolites, and 2014 reactions. Constraint-based analysis was used to characterize and evaluate the critical intracellular pathways...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800583/the-nucleoid-protein-dps-binds-genomic-dna-of-escherichia-coli-in-a-non-random-manner
#6
S S Antipov, M N Tutukina, E V Preobrazhenskaya, F A Kondrashov, M V Patrushev, S V Toshchakov, I Dominova, U S Shvyreva, V V Vrublevskaya, O S Morenkov, N A Sukharicheva, V V Panyukov, O N Ozoline
Dps is a multifunctional homododecameric protein that oxidizes Fe2+ ions accumulating them in the form of Fe2O3 within its protein cavity, interacts with DNA tightly condensing bacterial nucleoid upon starvation and performs some other functions. During the last two decades from discovery of this protein, its ferroxidase activity became rather well studied, but the mechanism of Dps interaction with DNA still remains enigmatic. The crucial role of lysine residues in the unstructured N-terminal tails led to the conventional point of view that Dps binds DNA without sequence or structural specificity...
2017: PloS One
https://www.readbyqxmd.com/read/28800137/chemical-dispersants-enhance-the-activity-of-oil-and-gas-condensate-degrading-marine-bacteria
#7
Julien Tremblay, Etienne Yergeau, Nathalie Fortin, Susan Cobanli, Miria Elias, Thomas L King, Kenneth Lee, Charles W Greer
Application of chemical dispersants to oil spills in the marine environment is a common practice to disperse oil into the water column and stimulate oil biodegradation by increasing its bioavailability to indigenous bacteria capable of naturally metabolizing hydrocarbons. In the context of a spill event, the biodegradation of crude oil and gas condensate off eastern Canada is an essential component of a response strategy. In laboratory experiments, we simulated conditions similar to an oil spill with and without the addition of chemical dispersant under both winter and summer conditions and evaluated the natural attenuation potential for hydrocarbons in near-surface sea water from the vicinity of crude oil and natural gas production facilities off eastern Canada...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28799667/coadministration-of-isomalto-oligosaccharides-augments-metabolic-health-benefits-of-cinnamaldehyde-in-high-fat-diet-fed-mice
#8
Dhirendra Pratap Singh, Pragyanshu Khare, Vandana Bijalwan, Ritesh Kumar Baboota, Jagdeep Singh, Kanthi Kiran Kondepudi, Kanwaljit Chopra, Mahendra Bishnoi
Bacteriostatic properties of a potential anti-obesity agent cinnamaldehyde (CMN) may present untoward effects on the resident gut microbiota. Here, we evaluated whether the combination of Isomalto-oligosaccharides (IMOs) with CMN prevents unwanted effects of CMN on gut microbiota and associated metabolic outcomes in HFD-fed mice. Male Swiss albino mice divided into four groups (n = 10), were fed on normal chow, or HFD (58% fat kcal), HFD + CMN (10 mg kg(-1) ) and HFD + CMN (10 mg kg(-1) ) + IMOs (1 g kg(-1) ) for 12 weeks...
August 11, 2017: BioFactors
https://www.readbyqxmd.com/read/28799224/genomic-insights-into-the-pathogenicity-and-environmental-adaptability-of-enterococcus-hirae-r17-isolated-from-pork-offered-for-retail-sale
#9
Zixin Peng, Menghan Li, Wei Wang, Hongtao Liu, Séamus Fanning, Yujie Hu, Jianzhong Zhang, Fengqin Li
Genetic information about Enterococcus hirae is limited, a feature that has compromised our understanding of these clinically challenging bacteria. In this study, comparative analysis was performed of E. hirae R17, a daptomycin-resistant strain isolated from pork purchased from a retail market in Beijing, China, and three other enterococcal genomes (Enterococcus faecium DO, Enterococcus faecalis V583, and E. hirae ATCC(™) 9790). Some 1,412 genes were identified that represented the core genome together with an additional 139 genes that were specific to E...
August 10, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28798729/in-silico-evolution-of-lysis-lysogeny-strategies-reproduces-observed-lysogeny-propensities-in-temperate-bacteriophages
#10
Vaibhhav Sinha, Akshit Goyal, Sine L Svenningsen, Szabolcs Semsey, Sandeep Krishna
Bacteriophages are the most abundant organisms on the planet and both lytic and temperate phages play key roles as shapers of ecosystems and drivers of bacterial evolution. Temperate phages can choose between (i) lysis: exploiting their bacterial hosts by producing multiple phage particles and releasing them by lysing the host cell, and (ii) lysogeny: establishing a potentially mutually beneficial relationship with the host by integrating their chromosome into the host cell's genome. Temperate phages exhibit lysogeny propensities in the curiously narrow range of 5-15%...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798696/phylogenetic-and-molecular-evolutionary-analysis-of-mitophagy-receptors-under-hypoxic-conditions
#11
Xiaomei Wu, Fei-Hua Wu, Qianrong Wu, Shu Zhang, Suping Chen, Matthew Sima
As animals evolved to use oxygen as the main strategy to produce ATP through the process of mitochondrial oxidative phosphorylation, the ability to adapt to fluctuating oxygen concentrations is a crucial component of evolutionary pressure. Three mitophagy receptors, FUNDC1, BNIP3 and NIX, induce the removal of dysfunctional mitochondria (mitophagy) under prolonged hypoxic conditions in mammalian cells, to maintain oxygen homeostasis and prevent cell death. However, the evolutionary origins and structure-function relationships of these receptors remain poorly understood...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28798165/complete-genome-sequences-of-three-isolates-of-xanthomonas-fragariae-the-bacterium-responsible-for-angular-leaf-spots-on-strawberry-plants
#12
Michael Gétaz, Jan M van der Wolf, Jochen Blom, Joël F Pothier
Xanthomonas fragariae is a worldwide-spread plant bacterial disease causing angular leaf spots, thus reducing the yield of production for strawberry fruits. Three isolates with various geographic and time origins were sequenced with long-read technology (PacBio) to generate finished genome sequences of virulent strains and observe the variability in their contents.
August 10, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28797211/disulfide-bonds-a-key-modification-in-bacterial-extracytoplasmic-proteins
#13
S F Lee, L Davey
Disulfide bonds are a common posttranslational modification that contributes to the folding and stability of extracytoplasmic proteins. Almost all organisms, from eukaryotes to prokaryotes, have evolved enzymes to make and break these bonds. Accurate and efficient disulfide bond formation can be vital for protein function; therefore, the enzymes that catalyze disulfide bond formation are involved in multiple biological processes. Recent advances clearly show that oral bacteria also have the ability to from disulfide bonds, and this ability has an effect on a range of dental plaque-related phenotypes...
August 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28797043/next-generation-sequencing-reveals-the-antibiotic-resistant-variants-in-the-genome-of-pseudomonas-aeruginosa
#14
Babu Ramanathan, Hassan Mahmood Jindal, Cheng Foh Le, Ranganath Gudimella, Arif Anwar, Rozaimi Razali, Johan Poole-Johnson, Rishya Manikam, Shamala Devi Sekaran
Rapid progress in next generation sequencing and allied computational tools have aided in identification of single nucleotide variants in genomes of several organisms. In the present study, we have investigated single nucleotide polymorphism (SNP) in ten multi-antibiotic resistant Pseudomonas aeruginosa clinical isolates. All the draft genomes were submitted to Rapid Annotations using Subsystems Technology (RAST) web server and the predicted protein sequences were used for comparison. Non-synonymous single nucleotide polymorphism (nsSNP) found in the clinical isolates compared to the reference genome (PAO1), and the comparison of nsSNPs between antibiotic resistant and susceptible clinical isolates revealed insights into the genome variation...
2017: PloS One
https://www.readbyqxmd.com/read/28794988/whole-genome-sequencing-of-microbacterium-sp-aiso3-from-polluted-san-jacinto-river-sediment-reveals-high-bacterial-mobility-metabolic-versatility-and-heavy-metal-resistance
#15
Rupa Iyer, Ashish Damania, Brian Iken
The genus Microbacterium is composed of high GC content, Gram-positive bacteria of the phylum Acintobacteria known for their antibiotic production. Microbacterium species commonly colonize agricultural rhizospheres and more infrequently have been found to colonize and infect human tissues as well. Here we report the 3,696,310 bp draft genome (chromosome and plasmids) sequence assembled at the scaffold level from 232 contigs of Microbacterium sp. strain AISO3, isolated from polluted San Jacinto River sediment in Channelview, Texas...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/28794225/the-divided-bacterial-genome-structure-function-and-evolution
#16
REVIEW
George C diCenzo, Turlough M Finan
Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella, Vibrio, and Burkholderia. The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome...
September 2017: Microbiology and Molecular Biology Reviews: MMBR
https://www.readbyqxmd.com/read/28794031/combinatorial-effects-of-the-glucocorticoid-receptor-and-kr%C3%A3-ppel-like-transcription-factor-15-on-bovine-herpesvirus-1-transcription-and-productive-infection
#17
Fouad S El-Mayet, Laximan Sawant, Prasanth Thunuguntla, Clinton Jones
Bovine herpesvirus 1 (BoHV-1), an important bovine pathogen, establishes life-long latency in sensory neurons. Latently infected calves consistently reactivate from latency following a single intravenous injection of the synthetic corticosteroid dexamethasone. The immediate early transcription unit 1 (IEtu1) promoter, which drives bICP0 and bICP4 expression, is stimulated by dexamethasone because it contains two glucocorticoid receptor (GR) response elements (GREs). Several Krüppel-like transcription factors (KLF), including KLF15, are induced during reactivation from latency and they stimulate certain viral promoters and productive infection...
August 9, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28793862/physical-shearing-imparts-biological-activity-to-dna-and-ability-to-transmit-itself-horizontally-across-species-and-kingdom-boundaries
#18
Gorantla Venkata Raghuram, Deepika Gupta, Siddharth Subramaniam, Ashwini Gaikwad, Naveen Kumar Khare, Malcolm Nobre, Naveen Kumar Nair, Indraneel Mittra
BACKGROUND: We have recently reported that cell-free DNA (cfDNA) fragments derived from dying cells that circulate in blood are biologically active molecules and can readily enter into healthy cells to activate DNA damage and apoptotic responses in the recipients. However, DNA is not conventionally known to spontaneously enter into cells or to have any intrinsic biological activity. We hypothesized that cellular entry and acquisition of biological properties are functions of the size of DNA...
August 9, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28793223/constraint-and-contingency-pervade-the-emergence-of-novel-phenotypes-in-complex-metabolic-systems
#19
Sayed-Rzgar Hosseini, Andreas Wagner
An evolutionary constraint is a bias or limitation in phenotypic variation that a biological system produces. We know examples of such constraints, but we have no systematic understanding about their extent and causes for any one biological system. We here study metabolisms, genomically encoded complex networks of enzyme-catalyzed biochemical reactions, and the constraints they experience in bringing forth novel phenotypes that allow survival on novel carbon sources. Our computational approach does not limit us to analyzing constrained variation in any one organism, but allows us to quantify constraints experienced by any metabolism...
August 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28792800/national-antimicrobial-resistance-monitoring-system-two-decades-of-advancing-public-health-through-integrated-surveillance-of-antimicrobial-resistance
#20
Beth E Karp, Heather Tate, Jodie R Plumblee, Uday Dessai, Jean M Whichard, Eileen L Thacker, Kis Robertson Hale, Wanda Wilson, Cindy R Friedman, Patricia M Griffin, Patrick F McDermott
Drug-resistant bacterial infections pose a serious and growing public health threat globally. In this review, we describe the role of the National Antimicrobial Resistance Monitoring System (NARMS) in providing data that help address the resistance problem and show how such a program can have broad positive impacts on public health. NARMS was formed two decades ago to help assess the consequences to human health arising from the use of antimicrobial drugs in food animal production in the United States. A collaboration among the Centers for Disease Control and Prevention, the U...
August 9, 2017: Foodborne Pathogens and Disease
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