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Dps (DNA binding proteins from starved cells)

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https://www.readbyqxmd.com/read/27091987/hysteresis-in-dna-compaction-by-dps-is-described-by-an-ising-model
#1
Natalia N Vtyurina, David Dulin, Margreet W Docter, Anne S Meyer, Nynke H Dekker, Elio A Abbondanzieri
In all organisms, DNA molecules are tightly compacted into a dynamic 3D nucleoprotein complex. In bacteria, this compaction is governed by the family of nucleoid-associated proteins (NAPs). Under conditions of stress and starvation, an NAP called Dps (DNA-binding protein from starved cells) becomes highly up-regulated and can massively reorganize the bacterial chromosome. Although static structures of Dps-DNA complexes have been documented, little is known about the dynamics of their assembly. Here, we use fluorescence microscopy and magnetic-tweezers measurements to resolve the process of DNA compaction by Dps...
May 3, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27021559/single-cell-analysis-of-the-dps-response-to-oxidative-stress
#2
Michela De Martino, Dmitry Ershov, Peter J van den Berg, Sander J Tans, Anne S Meyer
UNLABELLED: Microorganisms have developed an elaborate spectrum of mechanisms to respond and adapt to environmental stress conditions. Among these is the expression of dps, coding for the DNA-binding protein from starved cells. Dps becomes the dominant nucleoid-organizing protein in stationary-phase Escherichia coli cells and is required for robust survival under stress conditions, including carbon or nitrogen starvation, oxidative stress, metal exposure, and irradiation. To study the complex regulation of Dps in E...
June 1, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/26290287/dps-from-deinococcus-radiodurans-oligomeric-forms-of-dps1-with-distinct-cellular-functions-and-dps2-involved-in-metal-storage
#3
Sandra P Santos, Edward P Mitchell, Henri G Franquelim, Miguel A R B Castanho, Isabel A Abreu, Célia V Romão
The DNA binding proteins from starved cells from Deinococcus radiodurans, Dps1-DR2263 and Dps2-DRB0092, have a common overall structure of hollow spherical dodecamers. Their involvement in the homeostasis of intracellular metal and DNA protection was addressed. Our results show that DrDps proteins are able to oxidize ferrous to ferric iron by oxygen or hydrogen peroxide. The iron stored inside the hollow sphere cavity is fully released. Furthermore, these proteins are able to store and release manganese, suggesting they can play a role in manganese homeostasis as well...
November 2015: FEBS Journal
https://www.readbyqxmd.com/read/26216848/the-dna-binding-protein-from-starved-cells-dps-utilizes-dual-functions-to-defend-cells-against-multiple-stresses
#4
Vlad O Karas, Ilja Westerlaken, Anne S Meyer
UNLABELLED: Bacteria deficient in the DNA-binding protein from starved cells (Dps) are viable under controlled conditions but show dramatically increased mortality rates when exposed to any of a wide range of stresses, including starvation, oxidative stress, metal toxicity, or thermal stress. It remains unclear whether the protective action of Dps against specific stresses derives from its DNA-binding activity, which may exclude destructive agents from the chromosomal region, or its ferroxidase activity, which neutralizes and sequesters potentially damaging chemical species...
October 2015: Journal of Bacteriology
https://www.readbyqxmd.com/read/26208826/growth-phase-dependent-changes-in-the-structure-and-protein-composition-of-nucleoid-in-escherichia-coli
#5
AliAzam Talukder, Akira Ishihama
The genomic DNA of bacteria is highly compacted in a single or a few bodies known as nucleoids. Here, we have isolated Escherichia coli nucleoid by sucrose density gradient centrifugation. The sedimentation rates, structures as well as protein/ DNA composition of isolated nucleoids were then compared under various growth phases. The nucleoid structures were found to undergo changes during the cell growth; i. e., the nucleoid structure in the stationary phase was more tightly compacted than that in the exponential phase...
September 2015: Science China. Life Sciences
https://www.readbyqxmd.com/read/25707373/purification-of-the-campylobacter-jejuni-dps-protein-assisted-by-its-high-melting-temperature
#6
Heloisa B S Sanchuki, Glaucio Valdameri, Vivian R Moure, Marco A Oliveira, Fábio O Pedrosa, Emanuel M Souza, Victoria Korolik, Luciano F Huergo
Dps proteins (DNA binding protein from starved cell) form a distinct group within the ferritin superfamily. All Dps members are composed of 12 identical subunits that assemble into a conserved spherical protein shell. Dps oxidize Fe(2+) in a conserved ferroxidase center located at the interface between monomers, the product of the reaction Fe(3+), is then stored inside the protein shell in the form of non-reactive insoluble Fe2O3. The Campylobacter jejuni Dps (CjDps) has been reported to play a plethora of functions, such as DNA binding and protection, iron storage, survival in response to hydrogen peroxide and sulfatide binding...
July 2015: Protein Expression and Purification
https://www.readbyqxmd.com/read/25663155/differential-transcriptional-regulation-of-orthologous-dps-genes-from-two-closely-related-heterocyst-forming-cyanobacteria
#7
Xin Li, Gustaf Sandh, Anja Nenninger, Alicia M Muro-Pastor, Karin Stensjö
In cyanobacteria, DNA-binding proteins from starved cells (Dps) play an important role in the cellular response to oxidative and nutritional stresses. In this study, we have characterized the cell-type specificity and the promoter regions of two orthologous dps genes, Npun_R5799 in Nostoc punctiforme and alr3808 in Anabaena sp. PCC 7120. A transcriptional start site (TSS), identical in location to the previously identified proximal TSS of alr3808, was identified for Npun_R5799 under both combined nitrogen supplemented and N2-fixing growth conditions...
March 2015: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/24928392/a-perr-like-protein-involved-in-response-to-oxidative-stress-in-the-extreme-bacterium-deinococcus-radiodurans
#8
Chengzhi Liu, Liangyan Wang, Tao Li, Lin Lin, Shang Dai, Bing Tian, Yuejin Hua
Response and defense systems against reactive oxygen species (ROS) contribute to the remarkable resistance of Deinococcus radiodurans to oxidative stress induced by oxidants or radiation. However, mechanisms involved in ROS response and defense systems of D. radiodurans are not well understood. Fur family proteins are important in ROS response. Only a single Fur homolog is predicted by sequence similarity in the current D. radiodurans genome database. Our bioinformatics analysis demonstrated an additional guanine nucleotide in the genome of D...
July 18, 2014: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/24573673/a-histidine-aspartate-ionic-lock-gates-the-iron-passage-in-miniferritins-from-mycobacterium-smegmatis
#9
Sunanda Margrett Williams, Anu V Chandran, Mahalingam S Vijayabaskar, Sourav Roy, Hemalatha Balaram, Saraswathi Vishveshwara, Mamannamana Vijayan, Dipankar Chatterji
Dps (DNA-binding protein from starved cells) are dodecameric assemblies belonging to the ferritin family that can bind DNA, carry out ferroxidation, and store iron in their shells. The ferritin-like trimeric pore harbors the channel for the entry and exit of iron. By representing the structure of Dps as a network we have identified a charge-driven interface formed by a histidine aspartate cluster at the pore interface unique to Mycobacterium smegmatis Dps protein, MsDps2. Site-directed mutagenesis was employed to generate mutants to disrupt the charged interactions...
April 18, 2014: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/23748794/application-of-an-in-vitro-dna-protection-assay-to-visualize-stress-mediation-properties-of-the-dps-protein
#10
Vlad O Karas, Ilja Westerlaken, Anne S Meyer
Oxidative stress is an unavoidable byproduct of aerobic life. Molecular oxygen is essential for terrestrial metabolism, but it also takes part in many damaging reactions within living organisms. The combination of aerobic metabolism and iron, which is another vital compound for life, is enough to produce radicals through Fenton chemistry and degrade cellular components. DNA degradation is arguably the most damaging process involving intracellular radicals, as DNA repair is far from trivial. The assay presented in this article offers a quantitative technique to measure and visualize the effect of molecules and enzymes on radical-mediated DNA damage...
2013: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/23396000/kineococcus-radiotolerans-dps-forms-a-heteronuclear-mn-fe-ferroxidase-center-that-may-explain-the-mn-dependent-protection-against-oxidative-stress
#11
Matteo Ardini, Annarita Fiorillo, Maria Fittipaldi, Simonetta Stefanini, Dante Gatteschi, Andrea Ilari, Emilia Chiancone
BACKGROUND: The ferroxidase center of DNA-binding protein from starved cells (Dps) is a major player in the iron oxidation/detoxification process that leads to a decreased reactive oxygen species production. The possible Mn(II) participation in this process has been studied in Dps from Kineococcus radiotolerans, a radiation-resistant bacterium with a high cytosolic Mn/Fe ratio and a high capacity to survive ionizing and stress conditions. METHODS: The X-ray structure of recombinant K...
June 2013: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/23208094/aptamer-microarray-as-a-novel-bioassay-for-protein-protein-interaction-discovery-and-analysis
#12
Lin-Chi Chen, Shin-Cheng Tzeng, Konan Peck
Aptamer microarray is investigated as a novel bioassay for protein-protein interaction (PPI) discovery and analysis. Assaying a mixture of fluorescence-labeled thrombin and Escherichia coli proteins with an aptamer microarray, we found that thrombin and an unknown protein of E. coli (protein X) formed a complex of PPI, which was captured by an anti-thrombin aptamer probe. The PPI observed on the microarray was double-checked by protein microarrays and confirmed by aptamer-baited co-immunoprecipitation (Co-IP) assays...
April 15, 2013: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/23086936/the-role-of-heme-binding-by-dna-protective-protein-from-starved-cells-dps-in-the-tolerance-of-porphyromonas-gingivalis-to-heme-toxicity
#13
Jin-Long Gao, Yanling Lu, Gina Browne, Benjamin C-M Yap, Jill Trewhella, Neil Hunter, Ky-Anh Nguyen
The widely expressed DNA-protective protein from starved-cells (Dps) family proteins are considered major contributors to prokaryotic resistance to stress. We show here that Porphyromonas gingivalis Dps (PgDps), previously described as an iron-storage and DNA-binding protein, also mediates heme sequestration. We determined that heme binds strongly to PgDps with an apparent K(d) of 3.7 × 10(-8) m and is coordinated by a single surface-located cysteine at the fifth axial ligand position. Heme and iron sequestered in separate sites by PgDps provide protection of DNA from H(2)O(2)-mediated free radical damage and were found to be important for growth of P...
December 7, 2012: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/23061404/a-novel-iron-and-copper-binding-protein-in-the-lyme-disease-spirochaete
#14
Peng Wang, Anthony Lutton, John Olesik, Hojatollah Vali, Xin Li
Iron and copper are transition metals that can be toxic to cells due to their abilities to react with peroxide to generate hydroxyl radical. Ferritins and metallothioneins are known to sequester intracellular iron and copper respectively. The Lyme disease pathogen Borrelia burgdorferi does not require iron, but its genome encodes a ferritin-like Dps (DNA-binding protein from starved bacteria) molecule, which has been shown to be important for the spirochaete's persistence in the tick and subsequent transmission to a new host...
December 2012: Molecular Microbiology
https://www.readbyqxmd.com/read/22919649/dps-promotes-survival-of-nontypeable-haemophilus-influenzae-in-biofilm-communities-in-vitro-and-resistance-to-clearance-in-vivo
#15
Bing Pang, Wenzhou Hong, Nancy D Kock, W Edward Swords
Nontypeable Haemophilus influenzae (NTHi) is a common airway commensal and opportunistic pathogen that persists within surface-attached biofilm communities. In this study, we tested the hypothesis that bacterial stress-responses are activated within biofilms. Transcripts for several factors associated with bacterial resistance to environmental stress were increased in biofilm cultures as compared to planktonic cultures. Among these, a homolog of the DNA-binding protein from starved cells (dps) was chosen for further study...
2012: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/22837304/the-all0458-lti46-2-gene-encodes-a-low-temperature-induced-dps-protein-homologue-in-the-cyanobacteria-anabaena-sp-pcc-7120-and-anabaena-variabilis-m3
#16
Naoki Sato, Takashi Moriyama, Masakazu Toyoshima, Mika Mizusawa, Naoyuki Tajima
DNA-binding proteins from starved cells (Dps), which are encoded by many bacterial genomes, protect genomic DNA via non-specific DNA binding, as well as inhibition of free radical formation by chelating Fe(II). In the filamentous cyanobacterium Anabaena, the second gene (lti46.2) in the low temperature-induced gene operon lti46 in strain M3 was found to encode a homologue of Dps, but for a long time this gene remained poorly characterized. A gene cluster, all0459-all0458-all0457, was found later to be 100% identical to the lti46 gene cluster in a closely related strain, PCC 7120...
October 2012: Microbiology
https://www.readbyqxmd.com/read/22787197/the-campylobacter-jejuni-dps-homologue-is-important-for-in-vitro-biofilm-formation-and-cecal-colonization-of-poultry-and-may-serve-as-a-protective-antigen-for-vaccination
#17
James R Theoret, Kerry K Cooper, Bereket Zekarias, Kenneth L Roland, Bibiana F Law, Roy Curtiss, Lynn A Joens
In this work, we investigated the Campylobacter jejuni dps (DNA binding protein from starved cells) gene for a role in biofilm formation and cecal colonization in poultry. In vitro biofilm formation assays were conducted with stationary-phase cells in cell culture plates under microaerophilic conditions. These studies demonstrated a significant (>50%) reduction in biofilm formation by the C. jejuni dps mutant compared to that by the wild-type strain. Studies in poultry also demonstrated the importance of the dps gene in host colonization by C...
September 2012: Clinical and Vaccine Immunology: CVI
https://www.readbyqxmd.com/read/22739810/a-novel-mechanism-of-iron-core-formation-by-pyrococcus-furiosus-archaeoferritin-a-member-of-an-uncharacterized-branch-of-the-ferritin-like-superfamily
#18
Kourosh Honarmand Ebrahimi, Peter-Leon Hagedoorn, Laura van der Weel, Peter D E M Verhaert, Wilfred R Hagen
Storage of iron in a nontoxic and bioavailable form is essential for many forms of life. Three subfamilies of the ferritin-like superfamily, namely, ferritin, bacterioferritin, and Dps (DNA-binding proteins from starved cells), are able to store iron. Although the function of these iron-storage proteins is constitutive to many organisms to sustain life, the genome of some organisms appears not to encode any of these proteins. In an attempt to identify new iron-storage systems, we have found and characterized a new member of the ferritin-like superfamily of proteins, which unlike the multimeric storage system of ferritin, bacterioferritin, and Dps is monomeric in the absence of iron...
August 2012: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/22642556/desulfovibrio-vulgaris-bacterioferritin-uses-h-2-o-2-as-a-co-substrate-for-iron-oxidation-and-reveals-dps-like-dna-protection-and-binding-activities
#19
Cristina G Timóteo, Márcia Guilherme, Daniela Penas, Filipe Folgosa, Pedro Tavares, Alice S Pereira
A gene encoding Bfr (bacterioferritin) was identified and isolated from the genome of Desulfovibrio vulgaris cells, and overexpressed in Escherichia coli. In vitro, H(2)O(2) oxidizes Fe(2+) ions at much higher reaction rates than O(2). The H(2)O(2) oxidation of two Fe(2+) ions was proven by Mössbauer spectroscopy of rapid freeze-quenched samples. On the basis of the Mössbauer parameters of the intermediate species we propose that D. vulgaris Bfr follows a mineralization mechanism similar to the one reported for vertebrate H-type ferritins subunits, in which a diferrous centre at the ferroxidase site is oxidized to diferric intermediate species, that are subsequently translocated into the inner nanocavity...
August 15, 2012: Biochemical Journal
https://www.readbyqxmd.com/read/22454608/coevolution-of-aah-a-dps-like-gene-with-the-host-bacterium-revealed-by-comparative-genomic-analysis
#20
Liyan Ping, Matthias Platzer, Gaiping Wen, Nicolas Delaroque
A protein named AAH was isolated from the bacterium Microbacterium arborescens SE14, a gut commensal of the lepidopteran larvae. It showed not only a high sequence similarity to Dps-like proteins (DNA-binding proteins from starved cell) but also reversible hydrolase activity. A comparative genomic analysis was performed to gain more insights into its evolution. The GC profile of the aah gene indicated that it was evolved from a low GC ancestor. Its stop codon usage was also different from the general pattern of Actinobacterial genomes...
2012: TheScientificWorldJournal
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