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https://www.readbyqxmd.com/read/28104332/a-bacillus-sp-strain-with-antagonistic-activity-against-fusarium-graminearum-kills-microcystis-aeruginosa-selectively
#1
Huanling Xuan, Xianzhu Dai, Jing Li, Xiaohui Zhang, Caiyun Yang, Feng Luo
Cyanobacterial harmful algal blooms (CyanoHABs) cause severe environmental problems, economic losses and threaten human health seriously. In the present study, a Bacillus sp. strain, designated as AF-1, with strong antagonistic activity against plant pathogenic fungus Fusarium graminearum was isolated from purple soil. Bacillus sp. AF-1 selectively killed Microcystis aeruginosa at low cell density (1.6×10(3)cfu/mL), and showed the strongest bactericidal activity against M. aeruginosa NIES-843 (Ae=93%, t=6d)...
January 16, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28101376/atpase-activity-tightly-regulates-reca-nucleofilaments-to-promote-homologous-recombination
#2
Bailin Zhao, Dapeng Zhang, Chengmin Li, Zheng Yuan, Fangzhi Yu, Shangwei Zhong, Guibin Jiang, Yun-Gui Yang, X Chris Le, Michael Weinfeld, Ping Zhu, Hailin Wang
Homologous recombination (HR), catalyzed in an evolutionarily conserved manner by active RecA/Rad51 nucleofilaments, maintains genomic integrity and promotes biological evolution and diversity. The structures of RecA/Rad51 nucleofilaments provide information critical for the entire HR process. By exploiting a unique capillary electrophoresis-laser-induced fluorescence polarization assay, we have discovered an active form of RecA nucleofilament, stimulated by ATP hydrolysis, that contains mainly unbound nucleotide sites...
2017: Cell Discovery
https://www.readbyqxmd.com/read/28097539/rhizobium-hedysari-sp-nov-a-novel-species-isolated-from-a-root-nodule-of-hedysarum-multijugum-in-china
#3
Lin Xu, Jianfeng Shi, Caixia Li, Shengan Zhu, Bo Li
A strain 5-1-2(T) was isolated from a root nodule of Hedysarum multijugum collected from Zhangye city, Gansu province, north-west China. Phylogenetic analysis based on the 16S rRNA gene sequence and other housekeeping genes (recA and atpD) indicated that the strain represents a novel species in the genus Rhizobium close to the strain Rhizobium subbaraonis JC85(T) with similarities of 98.27, 88.92 and 89.62%, respectively. Strain 5-1-2(T) contained Q-10 as the predominant ubiquinone. Our results showed that the major fatty acids were feature 8 (C18:1 ω7c and/or C18:1 ω6c; 38...
January 17, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28096446/the-rpn-yhga-like-proteins-of-escherichia-coli-k-12-and-their-contribution-to-reca-independent-horizontal-transfer
#4
Anthony W Kingston, Christine Ponkratz, Elisabeth A Raleigh
: Bacteria use a variety of DNA mobilizing enzymes to facilitate environmental niche adaptation via horizontal gene transfer. This has led to real world problems, like the spread of antibiotic resistance, yet many mobilization proteins remain undefined. Here, we investigate the uncharacterized family of YhgA-like "transposase_31" proteins (PF04754). Our primary focus was the genetic and biochemical properties of the five E. coli K-12 members of this family, which we designate RpnA-RpnE for recombination promoting nuclease...
January 17, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28094097/diverse-genotypes-of-bradyrhizobium-nodulate-herbaceous-chamaecrista-moench-fabaceae-caesalpinioideae-species-in-brazil
#5
José Miguel Ferreira Dos Santos, Patricia Alves Casaes Alves, Verônica Cordeiro Silva, Mariana Ferreira Kruschewsky Rhem, Euan K James, Eduardo Gross
The genus Chamaecrista comprises more than 330 species which are mainly distributed across tropical America, especially in Brazil (256 spp.), the main center of radiation. In this study, nodulation of herbaceous Chamaecrista species that are commonly found growing in different vegetation types in the north eastern Brazilian state of Bahia was assessed together with the diversity of rhizobia isolated from their root nodules. Genetic characterization of the isolates was performed using molecular markers to examine the phylogeny of their "core" (16S rRNA, ITS, recA, glnII, dnaK and gyrB) and symbiosis-related (nifH, nodC) genomes...
January 10, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28092261/structural-insights-into-the-mechanism-of-the-deah-box-rna-helicase-prp43
#6
Marcel J Tauchert, Jean-Baptiste Fourmann, Reinhard Lührmann, Ralf Ficner
The DEAH-box helicase Prp43 is a key player in pre-mRNA splicing as well as the maturation of rRNAs. The exact modus operandi of Prp43 and of all other spliceosomal DEAH-box RNA helicases is still elusive. Here, we report crystal structures of Prp43 complexes in different functional states and the analysis of structure-based mutants providing insights into the unwinding and loading mechanism of RNAs. The Prp43•ATP-analog•RNA complex shows the localization of the RNA inside a tunnel formed by the two RecA-like and C-terminal domains...
January 16, 2017: ELife
https://www.readbyqxmd.com/read/28090586/holliday-junction-trap-shows-how-cells-use-recombination-and-a-junction-guardian-role-of-recq-helicase
#7
Jun Xia, Li-Tzu Chen, Qian Mei, Chien-Hui Ma, Jennifer A Halliday, Hsin-Yu Lin, David Magnan, John P Pribis, Devon M Fitzgerald, Holly M Hamilton, Megan Richters, Ralf B Nehring, Xi Shen, Lei Li, David Bates, P J Hastings, Christophe Herman, Makkuni Jayaram, Susan M Rosenberg
DNA repair by homologous recombination (HR) underpins cell survival and fuels genome instability, cancer, and evolution. However, the main kinds and sources of DNA damage repaired by HR in somatic cells and the roles of important HR proteins remain elusive. We present engineered proteins that trap, map, and quantify Holliday junctions (HJs), a central DNA intermediate in HR, based on catalytically deficient mutant RuvC protein of Escherichia coli. We use RuvCDefGFP (RDG) to map genomic footprints of HR at defined DNA breaks in E...
November 2016: Science Advances
https://www.readbyqxmd.com/read/28079255/moonlighting-at-replication-forks-a-new-life-for-homologous-recombination-proteins-brca1-brca2-and-rad51
#8
REVIEW
Arun Mouli Kolinjivadi, Vincenzo Sannino, Anna de Antoni, Hervé Técher, Giorgio Baldi, Vincenzo Costanzo
Coordination between DNA replication and DNA repair ensures maintenance of genome integrity, which is lost in cancer cells. Emerging evidence has linked Homologous Recombination (HR) proteins RAD51, BRCA1 and BRCA2 to the stability of nascent DNA. This function appears to be distinct from Double Strand Break (DSB) repair and is in part due to the prevention of MRE11-mediated degradation of nascent DNA at stalled forks. The role of RAD51 in fork protection resembles the activity described for its prokaryotic ortholog RecA, which prevents nuclease-mediated degradation of DNA and promotes replication fork restart in cells challenged by DNA damaging agents...
January 12, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28078720/the-intrinsically-disordered-linker-of-e-coli-ssb-is-critical-for-the-release-from-single-stranded-dna
#9
Hui Yin Tan, Luke A Wilczek, Sasheen Pottinger, Maria Manosas, Cong Yu, Trong Nguyenduc, Piero R Bianco
The Escherichia coli single stranded DNA binding protein (SSB) is crucial for DNA replication, recombination and repair. Within each process, it has two seemingly disparate roles: it stabilizes single-stranded DNA (ssDNA) intermediates generated during DNA processing and, forms complexes with a group of proteins known as the SSB-interactome. Key to both roles is the C-terminal, one-third of the protein, in particular the intrinsically disordered linker (IDL). Previously, we have shown using a series of linker deletion mutants that the IDL links both ssDNA and target protein binding by mediating interactions with the oligosaccharide/oligonucleotide binding fold in the target...
January 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28062461/diverse-bacteria-affiliated-with-the-genera-microvirga-phyllobacterium-and-bradyrhizobium-nodulate-lupinus-micranthus-growing-in-soils-of-northern-tunisia
#10
Abdelhakim Msaddak, David Durán, Mokhtar Rejili, Mohamed Mars, Tomás Ruiz-Argüeso, Juan Imperial, José Palacios, Luis Rey
: The genetic diversity of bacterial populations nodulating Lupinus micranthus in five geographical sites from Northern Tunisia was examined. Phylogenetic analyses of fifty isolates based on recA and gyrB gene partial sequences grouped strains in seven clusters, five of which belong to genus Bradyrhizobium (28 isolates), one to Phyllobacterium (2 isolates), and one, remarkably, to Microvirga (20 isolates). The largest Bradyrhizobium cluster (17 isolates) grouped with the B. lupini species and the other five clusters were close to different, recently defined Bradyrhizobium species...
January 6, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28056225/xenorhabdus-thuongxuanensis-sp-nov-and-xenorhabdus-eapokensis-sp-nov-isolated-from-steinernema-species
#11
Peter Kämpfer, Nicholas J Tobias, Long Phan Ke, Helge B Bode, Stefanie P Glaeser
Two slightly yellowish pigmented, oxidase-negative, rod-shaped and Gram-negative bacterial strains (30TX1T and DL20T), isolated from Steinernema sangi and Steinernema eapokense, respectively, during soil sampling in Vietnam were studied in a polyphasic taxonomic approach. Strain 30TX1T showed highest 16S rRNA gene sequence similarity to Xenorhabdus ehlersii (98.9%) and strain DL20T to Xenorhabdus ishibashii (98.7%). Sequence similarities to all other Xenorhabdus species were lower (< 98.4%). The two strains shared 98% 16S rRNA gene sequence similarity...
January 4, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28054431/dna-with-different-local-torsional-states-affects-reca-mediated-recombination-progression
#12
Chih-Hao Lu, Hung-Wen Li
DNA topology is thought to affect DNA enzyme activity. Helical structure of duplex DNA dictates the change of topological states during strand separation when DNA is constrained. During the repair of DNA double-stranded breaks, RecA nucleoprotein filament invades DNA and carries out consecutive strand exchange reactions, in coupling with duplex DNA strand separation. It has been suggested that torsional strain could be generated and its accumulation could inhibit strand exchange. We used hairpin and nicked DNA substrates to test how torsional strain alters the RecA-mediated strand exchange efficiency...
January 5, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28052848/pseudomonas-aeruginosa-oligoribonuclease-contributes-to-tolerance-to-ciprofloxacin-by-regulating-pyocin-biosynthesis
#13
Fei Chen, Gukui Chen, Yiwei Liu, Yongxin Jin, Zhihui Cheng, Yang Liu, Liang Yang, Shouguang Jin, Weihui Wu
Bacterial oligoribonuclease (Orn) is a conserved 3' to 5' exonuclease. In Pseudomonas aeruginosa, it has been demonstrated that Orn plays a major role in the hydrolysis of pGpG which is required for c-di-GMP homeostasis. Meanwhile, Orn is involved in the degradation of nanoRNAs which can alter global gene expression by serving as transcription initiation primers. Previously, we found that Orn is required for the type III secretion system and pathogenesis of P. aeruginosa, indicating a role of Orn in bacterial response to environmental stimuli...
January 4, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28049371/structure-and-interactions-of-reca-plasticity-revealed-by-molecular-dynamics-simulations
#14
Anu V Chandran, S Jayanthi, M Vijayan
Eleven independent simulations, each involving three consecutive molecules in the RecA filament, carried out on the protein from Mycobacterium tuberculosis, Mycobacterium smegmatis and Escherichia coli and their Adenosine triphosphate (ATP) complexes, provide valuable information which is complementary to that obtained from crystal structures, in addition to confirming the robust common structural framework within which RecA molecules from different eubacteria function. Functionally important loops, which are largely disordered in crystal structures, appear to adopt in each simulation subsets of conformations from larger ensembles...
January 4, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28039103/itraq-based-proteome-analysis-of-fluoroquinolone-resistant-staphylococcus-aureus
#15
Van Chi Thai, Teck Kwang Lim, Kim Phuong Uyen Le, Qingsong Lin, Thi Thu Hoai Nguyen
OBJECTIVES: The aim of this study was to compare global protein expression changes during fluoroquinolone (FQ) exposure of Staphylococcus aureus. METHODS: Total protein extracts of wild-type S. aureus ATCC 29213 and six multidrug-resistant (MDR) strains derived from the wild-type under different FQ exposures were analysed using the 8-plex isobaric tag for relative and absolute quantitation (iTRAQ) method combined with LC-MS/MS analysis. Differentially expressed proteins were searched for their Gene Ontology (GO) annotation (UniProt database) and protein-protein interaction network (STRING v...
December 27, 2016: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28032540/photorhabdus-luminescens-subsp-namnaonensis-subsp-nov-isolated-from-heterorhabditis-baujardi-nematodes-in-nam-nao-district-of-central-thailand
#16
Stefanie P Glaeser, Nicholas J Tobias, Aunchalee Thanwisai, Narisara Chantratita, Helge B Bode, Peter Kämpfer
A lightly yellowish pigmented, oxidase-negative bacterial strain (PB45.5T), isolated from the Nam Nao district of Phetchabun in central Thailand was investigated for its taxonomic position. The cells morphology of the isolate showed a rod shaped appearance. The strain stained Gram-negative. Strain PB45.5T shared highest 16S rRNA gene sequence similarity with the type strain of Photorhabdus luminescens subsp. akhurstii (99.2%) and Photorhabdus luminescens subsp. hainanensisi (99.1%) and lower similarities to all other Photorhabdus luminescens subspecies (< 98...
December 29, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28013513/the-interaction-of-antimicrobial-peptides-with-the-membrane-and-intracellular-targets-of-staphylococcus-aureus-investigated-by-atp-leakage-dna-binding-analysis-and-the-expression-of-a-lexa-controlled-gene-reca
#17
Sanne Gottschalk, Line Elnif Thomsen
The analysis of how antimicrobial peptides (AMPs) interact with bacterial membranes and intracellular targets is important for our understanding of how these molecules affect bacteria. Increased knowledge may aid the design of AMPs that work on their target bacterium without inducing bacterial resistance. Here, we describe different methods to investigate the mode of action of peptides against the Gram-positive bacterium Staphylococcus aureus. ATP leakage analysis can be used to evaluate the ability of AMPs to perturb bacteria...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28003197/elucidation-of-antibacterial-mechanism-of-405%C3%A2-5-nm-light-emitting-diode-against-salmonella-spp-at-refrigeration-temperature
#18
Min-Jeong Kim, Hyun-Gyun Yuk
: The aim of this study was to elucidate the antibacterial mechanism of 405±5 nm light-emitting diode (LED) illumination against Salmonella at 4 °C in phosphate-buffered saline (PBS) by determining endogenous coproporphyrin content, DNA oxidation, damage to membrane function, and morphological change. Gene expression levels, including oxyR, recA, rpoS, sodA, and soxR, were also examined to understand the response of Salmonella to LED illumination. Results showed that Salmonella spp...
December 21, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27990000/phenotypic-difference-between-%C3%AE-srl-reca-306-and-%C3%AE-reca-km-elucidated-by-next-generation-sequencing-combined-with-a-long-pcr-system
#19
Shingo Suzuki, Akihiro Kaidow, Takuma Meya, Anri Masuya, Takashi Shiina
Many significant gene mutations in E. coli have contributed to the development of genetics. Among these, a commonly used recA mutation, Δ(srl-recA)306 has been sequenced by a next-generation sequencer combined with a long PCR. An original report described that Δ(srl-recA)306 cells were deleted from srlR to recA genes in their genome. The next-generation sequencer enables more accurate details to be determined. We ask whether both surrounding genes from hypF to norV for srlR and alaS for recA is there first...
December 17, 2016: Journal of General and Applied Microbiology
https://www.readbyqxmd.com/read/27986727/burkholderia-humptydooensis-sp-nov-a-new-species-related-to-burkholderia-thailandensis-and-the-fifth-member-of-the-pseudomallei-complex
#20
Apichai Tuanyok, Mark Mayo, Holger Scholz, Carina M Hall, Christopher J Allender, Mirjam Kaestli, Jennifer Ginther, Senanu Spring-Pearson, Molly C Bollig, Joshua K Stone, Erik W Settles, Joseph D Busch, Lindsay Sidak-Loftis, Jason W Sahl, Astrid Thomas, Lisa Kreutzer, Enrico Georgi, Jay E Gee, Richard A Bowen, Jason T Ladner, Sean Lovett, Galina Koroleva, Gustavo Palacios, David M Wagner, Bart J Currie, Paul Keim
: During routine screening for endemic Burkholderia pseudomallei from water wells in northern Australia, Gram-staining-negative bacteria (strains MSMB43(T), MSMB121, and MSMB122) with a similar morphology and biochemical pattern to B. pseudomallei and B. thailandensis were co-isolated with B. pseudomallei on Ashdown's selective agar. To determine the exact taxonomic position of these strains and to distinguish them from B. pseudomallei and B. thailandensis, they were subjected to a series of phenotypic and molecular analyses...
December 16, 2016: Applied and Environmental Microbiology
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