scholarly journals Mechanisms of Action of Escapin, a Bactericidal Agent in the Ink Secretion of the Sea Hare Aplysia californica: Rapid and Long-Lasting DNA Condensation and Involvement of the OxyR-Regulated Oxidative Stress Pathway

2012 ◽  
Vol 56 (4) ◽  
pp. 1725-1734 ◽  
Author(s):  
Ko-Chun Ko ◽  
Phang C. Tai ◽  
Charles D. Derby
Keyword(s):  
Oxidative Stress ◽  
Carboxylic Acid ◽  
Dna Binding ◽  
Binding Protein ◽  
Aplysia Californica ◽  
Dna Binding Protein ◽  
Bactericidal Effect ◽  
Dna Condensation ◽  
Maximal Effect ◽  
Content Type

ABSTRACTThe marine snailAplysia californicaproduces escapin, anl-amino acid oxidase, in its defensive ink. Escapin usesl-lysine to produce diverse products called escapin intermediate products ofl-lysine (EIP-K), including α-amino-ε-caproic acid, Δ1-piperidine-2-carboxylic acid, and Δ2-piperidine-2-carboxylic acid. EIP-K and H2O2together, but neither alone, is a powerful bactericide. Here, we report bactericidal mechanisms of escapin products onEscherichia coli. We show that EIP-K and H2O2together cause rapid and long-lasting DNA condensation: 2-min treatment causes significant DNA condensation and killing, and 10-min treatment causes maximal effect, lasting at least 70 h. We isolated two mutants resistant to EIP-K plus H2O2, both having a single missense mutation in the oxidation regulatory gene,oxyR. A complementation assay showed that the mutated gene,oxyR(A233V), renders resistance to EIP-K plus H2O2, and a gene dosage effect leads to reduction of resistance for strains carrying wild-typeoxyR. Temperature stress with EIP-K does not produce the bactericidal effect, suggesting the effect is due to a specific response to oxidative stress. The null mutant for any single DNA-binding protein—Dps, H-NS, Hup, Him, or MukB—was not resistant to EIP-K plus H2O2, suggesting that no single DNA-binding protein is necessary to mediate this bactericidal effect, but allowing for the possibility that EIP-K plus H2O2could function through a combination of DNA-binding proteins. The bactericidal effect of EIP-K plus H2O2was eliminated by the ferrous ion chelator 1,10-phenanthroline, and it was reduced by the hydroxyl radical scavenger thiourea, suggesting hydroxyl radicals mediate the effects of EIP-K plus H2O2.

scholarly journals A Novel DNA-Binding Protein Plays an Important Role in Helicobacter pylori Stress Tolerance and Survival in the Host

2014 ◽  
Vol 197 (5) ◽  
pp. 973-982 ◽  
Author(s):  
Ge Wang ◽  
Robert J. Maier
Keyword(s):  
Oxidative Stress ◽  
Helicobacter Pylori ◽  
Dna Binding ◽  
Stress Tolerance ◽  
Mutant Strain ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Wild Type ◽  
Content Type ◽  
H Pylori

The gastric pathogenHelicobacter pylorimust combat chronic acid and oxidative stress. It does so via many mechanisms, including macromolecule repair and gene regulation. Mitomycin C-sensitive clones from a transposon mutagenesis library were screened. One sensitive strain contained the insertion element at the locus ofhp119, a hypothetical gene. No homologous gene exists in any (non-H. pylori) organism. Nevertheless, the predicted protein has some features characteristic of histone-like proteins, and we showed that purified HP119 protein is a DNA-binding protein. A Δhp119strain was markedly more sensitive (viability loss) to acid or to air exposure, and these phenotypes were restored to wild-type (WT) attributes upon complementation of the mutant with the wild-type version ofhp119at a separate chromosomal locus. The mutant strain was approximately10-fold more sensitive to macrophage-mediated killing than the parent or the complemented strain. Of 12 mice inoculated with the wild type, all containedH. pylori, whereas 5 of 12 mice contained the mutant strain; the mean colonization numbers were 158-fold less for the mutant strain. A proteomic (two-dimensional PAGE with mass spectrometric analysis) comparison between the Δhp119mutant and the WT strain under oxidative stress conditions revealed a number of important antioxidant protein differences; SodB, Tpx, TrxR, and NapA, as well as the peptidoglycan deacetylase PgdA, were significantly less expressed in the Δhp119mutant than in the WT strain. This study identified HP119 as a putative histone-like DNA-binding protein and showed that it plays an important role inHelicobacter pyloristress tolerance and survival in the host.

scholarly journals The DNA-Binding Protein from Starved Cells (Dps) Utilizes Dual Functions To Defend Cells against Multiple Stresses

2015 ◽  
Vol 197 (19) ◽  
pp. 3206-3215 ◽  
Author(s):  
Vlad O. Karas ◽  
Ilja Westerlaken ◽  
Anne S. Meyer
Keyword(s):  
Oxidative Stress ◽  
Dna Binding ◽  
Binding Protein ◽  
Protective Action ◽  
Iron Oxidation ◽  
Dna Binding Protein ◽  
Content Type ◽  
E Coli ◽  
Wide Range ◽  
Ferroxidase Activity

ABSTRACTBacteria 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. To resolve this question, we have identified the critical residues ofEscherichia coliDps that bind to DNA and modulate iron oxidation. We uncoupled the biochemical activities of Dps, creating Dps variants and mutantE. colistrains that are defective in either DNA-binding or ferroxidase activity. Quantification of the contribution of each activity to the protection of DNA integrity and cellular viability revealed that both activities of Dps are required in order to counteract many differing stresses. These findings demonstrate that Dps plays a multipurpose role in stress protection via its dual activities, explaining how Dps can be of vital importance to bacterial viability over a wide range of stresses.IMPORTANCEThe DNA-binding protein from starved cells (Dps) protects bacterial cells against many different types of stressors. We find that DNA binding and iron oxidation by Dps are performed completely independently of each other. Both biochemical activities are required to protectE. coliagainst stressors, as well as to protect DNA from oxidative damagein vitro. These results suggest that many stressors may cause both oxidative stress and direct DNA damage.

scholarly journals The Bacterial DNA Binding Protein MatP Involved in Linking the Nucleoid Terminal Domain to the Divisome at Midcell Interacts with Lipid Membranes

mBio ◽  
2019 ◽  
Vol 10 (3) ◽  
Author(s):  
Begoña Monterroso ◽  
Silvia Zorrilla ◽  
Marta Sobrinos-Sanguino ◽  
Miguel Ángel Robles-Ramos ◽  
Carlos Alfonso ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Sequences ◽  
Lipid Membranes ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Content Type ◽  
E Coli ◽  
Daughter Cells ◽  
Z Ring

ABSTRACTDivision ring formation at midcell is controlled by various mechanisms inEscherichia coli, one of them being the linkage between the chromosomal Ter macrodomain and the Z-ring mediated by MatP, a DNA binding protein that organizes this macrodomain and contributes to the prevention of premature chromosome segregation. Here we show that, during cell division, just before splitting the daughter cells, MatP seems to localize close to the cytoplasmic membrane, suggesting that this protein might interact with lipids. To test this hypothesis, we investigated MatP interaction with lipidsin vitro. We found that, when encapsulated inside vesicles and microdroplets generated by microfluidics, MatP accumulates at phospholipid bilayers and monolayers matching the lipid composition in theE. coliinner membrane. MatP binding to lipids was independently confirmed using lipid-coated microbeads and biolayer interferometry assays, which suggested that the recognition is mainly hydrophobic. Interaction of MatP with the lipid membranes also occurs in the presence of the DNA sequences specifically targeted by the protein, but there is no evidence of ternary membrane/protein/DNA complexes. We propose that the association of MatP with lipids may modulate its spatiotemporal localization and its recognition of other ligands.IMPORTANCEThe division of anE. colicell into two daughter cells with equal genomic information and similar size requires duplication and segregation of the chromosome and subsequent scission of the envelope by a protein ring, the Z-ring. MatP is a DNA binding protein that contributes both to the positioning of the Z-ring at midcell and the temporal control of nucleoid segregation. Our integratedin vivoandin vitroanalysis provides evidence that MatP can interact with lipid membranes reproducing the phospholipid mixture in theE. coliinner membrane, without concomitant recruitment of the short DNA sequences specifically targeted by MatP. This observation strongly suggests that the membrane may play a role in the regulation of the function and localization of MatP, which could be relevant for the coordination of the two fundamental processes in which this protein participates, nucleoid segregation and cell division.

Response of a DNA-binding Protein to Radiation-induced Oxidative Stress

2003 ◽  
Vol 328 (5) ◽  
pp. 1185-1195 ◽  
Author(s):  
Françoise Culard ◽  
Alain Gervais ◽  
Guillaume de Vuyst ◽  
Mélanie Spotheim-Maurizot ◽  
Michel Charlier
Keyword(s):  
Oxidative Stress ◽  
Dna Binding ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Radiation Induced

scholarly journals Chronic oxidative stress promotes GADD34-mediated phosphorylation of the TAR DNA-binding protein TDP-43, a modification linked to neurodegeneration

2017 ◽  
Vol 293 (1) ◽  
pp. 163-176 ◽  
Author(s):  
Catherine Wenhui Goh ◽  
Irene Chengjie Lee ◽  
Jeyapriya Rajameenakshi Sundaram ◽  
Simi Elizabeth George ◽  
Permeen Yusoff ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Dna Binding ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Chronic Oxidative Stress

scholarly journals Z-DNA Binding Protein Mediates Host Control of Toxoplasma gondii Infection

2016 ◽  
Vol 84 (10) ◽  
pp. 3063-3070 ◽  
Author(s):  
Kelly J. Pittman ◽  
Patrick W. Cervantes ◽  
Laura J. Knoll
Keyword(s):  
Immune Response ◽  
Toxoplasma Gondii ◽  
Dna Binding ◽  
Chronic Infection ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Host Immune Response ◽  
Activated Macrophages ◽  
Content Type ◽  
Z Dna

Intrinsic toToxoplasma gondiiinfection is the parasite-induced modulation of the host immune response, which ensures establishment of a chronic lifelong infection. This manipulation of the host immune response allowsT. gondiito not only dampen the ability of the host to eliminate the parasite but also trigger parasite differentiation to the slow-growing, encysted bradyzoite form. We previously used RNA sequencing (RNA-seq) to profile the transcriptomes of mice andT. gondiiduring acute and chronic stages of infection. One of the most abundant host transcripts during acute and chronic infection was Z-DNA binding protein 1 (ZBP1). In this study, we determined that ZBP1 functions to controlT. gondiigrowth. In activated macrophages isolated from ZBP1 deletion (ZBP1−/−) mice,T. gondiihas an increased rate of replication and a decreased rate of degradation. We also identified a novel function for ZBP1 as a regulator of nitric oxide (NO) production in activated macrophages, even in the absence ofT. gondiiinfection. Upon stimulation,T. gondii-infected ZBP1−/−macrophages display increased proinflammatory cytokines compared to wild-type macrophages under the same conditions. Thesein vitrophenotypes were recapitulatedin vivo, with ZBP1−/−mice having increased susceptibility to oral challenge, higher cyst burdens during chronic infection, and elevated inflammatory cytokine responses. Taken together, these results highlight a role for ZBP1 in assisting host control ofT. gondiiinfection.

scholarly journals The DUF328 family member YaaA is a DNA-binding protein with a novel fold

2020 ◽  
Vol 295 (41) ◽  
pp. 14236-14247
Author(s):  
Janani Prahlad ◽  
Yifeng Yuan ◽  
Jiusheng Lin ◽  
Chou-Wei Chang ◽  
Dirk Iwata-Reuyl ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Dna Repair ◽  
Stress Response ◽  
Dna Binding ◽  
Binding Protein ◽  
Equilibrium Constants ◽  
Dna Recombination ◽  
Dna Binding Protein ◽  
Oxidative Stress Response ◽  
Binding Motif

DUF328 family proteins are present in many prokaryotes; however, their molecular activities are unknown. The Escherichia coli DUF328 protein YaaA is a member of the OxyR regulon and is protective against oxidative stress. Because uncharacterized proteins involved in prokaryotic oxidative stress response are rare, we sought to learn more about the DUF328 family. Using comparative genomics, we found a robust association between the DUF328 family and genes involved in DNA recombination and the oxidative stress response. In some proteins, DUF328 domains are fused to other domains involved in DNA binding, recombination, and repair. Cofitness analysis indicates that DUF328 family genes associate with recombination-mediated DNA repair pathways, particularly the RecFOR pathway. Purified recombinant YaaA binds to dsDNA, duplex DNA containing bubbles of unpaired nucleotides, and Holliday junction constructs in vitro with dissociation equilibrium constants of 200–300 nm. YaaA binds DNA with positive cooperativity, forming multiple shifted species in electrophoretic mobility shift assays. The 1.65-Å resolution X-ray crystal structure of YaaA reveals that the protein possesses a new fold that we name the cantaloupe fold. YaaA has a positively charged cleft and a helix-hairpin-helix DNA-binding motif found in other DNA repair enzymes. Our results demonstrate that YaaA is a new type of DNA-binding protein associated with the oxidative stress response and that this molecular function is likely conserved in other DUF328 family members.

scholarly journals Sulfolobus Spindle-Shaped Virus 1 Contains Glycosylated Capsid Proteins, a Cellular Chromatin Protein, and Host-Derived Lipids

2015 ◽  
Vol 89 (22) ◽  
pp. 11681-11691 ◽  
Author(s):  
Emmanuelle R. J. Quemin ◽  
Maija K. Pietilä ◽  
Hanna M. Oksanen ◽  
Patrick Forterre ◽  
W. Irene C. Rijpstra ◽  
...  
Keyword(s):  
Dna Binding ◽  
Biochemical Characterization ◽  
Binding Protein ◽  
Structural Data ◽  
Dna Binding Protein ◽  
Ecological Niches ◽  
Chromatin Protein ◽  
Content Type ◽  
Cellular Origin

ABSTRACTGeothermal and hypersaline environments are rich in virus-like particles, among which spindle-shaped morphotypes dominate. Currently, viruses with spindle- or lemon-shaped virions are exclusive toArchaeaand belong to two distinct viral families. The larger of the two families, theFuselloviridae, comprises tail-less, spindle-shaped viruses, which infect hosts from phylogenetically distant archaeal lineages.Sulfolobusspindle-shaped virus 1 (SSV1) is the best known member of the family and was one of the first hyperthermophilic archaeal viruses to be isolated. SSV1 is an attractive model for understanding virus-host interactions inArchaea; however, the constituents and architecture of SSV1 particles remain only partially characterized. Here, we have conducted an extensive biochemical characterization of highly purified SSV1 virions and identified four virus-encoded structural proteins, VP1 to VP4, as well as one DNA-binding protein of cellular origin. The virion proteins VP1, VP3, and VP4 undergo posttranslational modification by glycosylation, seemingly at multiple sites. VP1 is also proteolytically processed. In addition to the viral DNA-binding protein VP2, we show that viral particles contain theSulfolobus solfataricuschromatin protein Sso7d. Finally, we provide evidence indicating that SSV1 virions contain glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, resolving a long-standing debate on the presence of lipids within SSV1 virions. A comparison of the contents of lipids isolated from the virus and its host cell suggests that GDGTs are acquired by the virus in a selective manner from the host cytoplasmic membrane, likely during progeny egress.IMPORTANCEAlthough spindle-shaped viruses represent one of the most prominent viral groups inArchaea, structural data on their virion constituents and architecture still are scarce. The comprehensive biochemical characterization of the hyperthermophilic virus SSV1 presented here brings novel and significant insights into the organization and architecture of spindle-shaped virions. The obtained data permit the comparison between spindle-shaped viruses residing in widely different ecological niches, improving our understanding of the adaptation of viruses with unusual morphotypes to extreme environmental conditions.

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