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Dps (DNA binding proteins from starved cells)

Thomas A Cornell, Maziar S Ardejani, Jing Fu, Stephanie H Newland, Yu Zhang, Brendan P Orner
Cage proteins, which assemble into often highly symmetric hollow nanoscale capsules, have great potential in applications as far reaching as drug delivery, hybrid nanomaterial engineering, and catalysis. In addition, they are promising model systems for understanding how cellular nanostructures are constructed through protein-protein interactions, and they are beginning to be used as scaffolds for synthetic biology approaches. Recently, there has been renewed interest in the engineering of protein cages, and in support of these strategies, we have recently described a fluorescence-based assay for protein cage assembly that is specific for certain oligomerization states and symmetry-related protein-protein interfaces...
February 6, 2018: Biochemistry
Yawei Ni, Jianhua Guo, Debra Turner, Ian Tizard
A highly effective antigen construct for presenting conserved antigen domains is essential to the development of a universal influenza vaccine. We have developed a novel dual-domain nanoparticle fusion protein (DDNFP) which allows independent presentation of two conserved domains. The conserved domains used were from two separate viral surface proteins, M2e of M2 and fusion peptide (FP) or long alpha helix (CD) of HA2. The carrier is a novel nanoparticle protein - the dodecameric DNA binding protein from starved cells (Dps) of bacteria or archaea...
December 15, 2017: Vaccine
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
Xiaoyun Xia, Jessie Larios-Valencia, Zhi Liu, Fu Xiang, Biao Kan, Hui Wang, Jun Zhu
Vibrio cholerae is the causative agent of cholera, a dehydrating diarrheal disease. This Gram-negative pathogen is able to modulate its gene expression in order to combat stresses encountered in both aquatic and host environments, including stress posed by reactive oxygen species (ROS). In order to further the understanding of V. cholerae's transcriptional response to ROS, we performed an RNA sequencing analysis to determine the transcriptional profile of V. cholerae when exposed to hydrogen hydroperoxide. Of 135 differentially expressed genes, VC0139 was amongst the genes with the largest induction...
2017: PloS One
Sandra P Santos, Maxime G Cuypers, Adam Round, Stephanie Finet, Theyencheri Narayanan, Edward P Mitchell, Célia V Romão
The radiation-resistant bacterium Deinococcus radiodurans contains two DNA-binding proteins from starved cells (Dps): Dps1 (DR2263) and Dps2 (DRB0092). These are suggested to play a role in DNA interaction and manganese and iron storage. The proteins assemble as a conserved dodecameric structure with structurally uncharacterised N-terminal extensions. In the case of DrDps1, these extensions have been proposed to be involved in DNA interactions, while in DrDps2, their function has yet to be established. The reported data reveal the relative position of the N-terminal extensions to the dodecameric sphere in solution for both Dps...
March 10, 2017: Journal of Molecular Biology
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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