Role of Dps (DNA-binding proteins from starved cells) aggregation on DNA

Frontiers in Bioscience

Volumn 15, Issue 1, 2010, Pages 122-131

  Chiancone, Emilia ^a   Ceci, Pierpaolo ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

Author keywords

Dps (DNA binding proteins from starved cells) proteins; Dps DNA interaction; Ferroxidase activity; Microbial survival; Nucleoid organization; Review

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; DNA BINDING PROTEIN; DPS PROTEIN, BACTERIA;

AMINO ACID SEQUENCE; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN QUATERNARY STRUCTURE; REVIEW; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; DNA, BACTERIAL; DNA-BINDING PROTEINS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 77951235336     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/3610     Document Type: Article

References (45)

1. T. A. Azam, A. Iwata, A. Nishimura, S. Ueda, A. Ishihama: Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181, 6361-6370 (1999). (Pubitemid 29512946)
2. J. Kim, S. H. Yoshimura, K. Hizume, R. L. Ohniwa, A. Ishihama, K. Takeyasu: Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy. Nucleic Acids Res 32, 1982-1992 (2004). (Pubitemid 38842538)
3. C. A. Ball, R. Osuna, K. C. Ferguson, R. C. Johnson: Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J Bacteriol 174, 8043-8056 (1992). (Pubitemid 23002939)
4. S. Altuvia, M. Almirón, G. Huisman, R. Kolter, G. Storz: The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase. Mol Microbiol 13, 265-272 (1994).
5. K. Morikawa, R. L. Ohniwa, J. Kim, A. Maruyama, T. Ohta, K. Takeyasu: Bacterial nucleoid dynamics: oxidative stress response in Staphylococcus aureus. Genes Cells 11, 409-423 (2006).
6. M. Ljungman, P. C. Hanawalt: Efficient protection against oxidative DNA damage in chromatin. Mol Carcinog 5, 264-269 (1992).
7. Y. Yoshikawa, K. Hizume, Y. Oda, K. Takeyasu, S. Araki, K. Yoshikawa: Protective effect of vitamin C against double-strand breaks in reconstituted chromatin visualized by single-molecule observation. Biophys J 90, 993-999 (2006).
8. S. Nair, S. E. Finkel: Dps protects cells against multiple stresses during stationary phase. J Bacteriol 186, 4192- 4198 (2004). (Pubitemid 38802567)
9. M. Almiron, A. J. Link, F. Deirdre, R. Kolter: A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev 6, 2646-2654 (1992). (Pubitemid 23052891)
10. A. Martinez, R. Kolter: Protection of DNA during oxidative stress by the nonspecific DNA-binding protein Dps. J Bacteriol 179, 5188-5194 (1997). (Pubitemid 27340555)
11. G. Zhao, P. Ceci, A. Ilari, L. Giangiacomo, T. M. Laue, E. Chiancone, N. D. Chasteen: Iron and hydrogen peroxide detoxification properties of DNA-binding protein from starved cells. A ferritin-like DNA-binding protein of Escherichia coli. J Biol Chem 277, 27689-27696 (2002). (Pubitemid 34966712)
12. P. Ceci, A. Ilari, E. Falvo, E. Chiancone: The Dps protein of Agrobacterium tumefaciens does not bind to DNA but protects it toward oxidative cleavage: x-ray crystal structure, iron binding, and hydroxyl-radical scavenging properties. J Biol Chem 278, 20319-2032 (2003).
13. 2 resistance mediated by Streptococcal Dpr. Demonstration of the functional involvement of the putative ferroxidase center by sitedirected mutagenesis in Streptococcus suis. J Biol Chem 278, 7996-8005 (2003). (Pubitemid 36800538)
14. A. Ilari, M. C. Latella, P. Ceci, F. Ribacchi, M. Su, L. Giangiacomo, S. Stefanini, N. D. Chasteen, E. Chiancone: The unusual intersubunit ferroxidase center of Listeria innocua Dps is required for hydrogen peroxide detoxification but not for iron uptake. A study with sitespecific mutants. Biochemistry 44, 5579-5587 (2005). (Pubitemid 40525095)
15. B. Ren, G. Tibbelin, T. Kajino, O. Asami, R. Ladenstein: The multi-layered structure of Dps with a novel di-nuclear ferroxidase center. J Mol Biol 329:467- 477 (2003). (Pubitemid 36593206)
16. R. A. Grant, D. J. Filman, S. E. Finkel, R. Kolter and J. M. Hogle: The crystal structure of Dps, a ferritin homolog that binds and protects DNA. Nat Struct Biol 5, 294-303 (1998). (Pubitemid 28164882)
17. W. Jin, H. Takagi, B. Pancorbo, E. C. Theil: "Opening" the ferritin pore for iron release by mutation of conserved amino acids at interhelix and loop sites. Biochemistry 40:7525-7532 (2001). (Pubitemid 32578017)
18. S. Franceschini, P. Ceci, F. Alaleona, E. Chiancone, A. Ilari: Antioxidant Dps protein from the thermophilic cyanobacterium Thermosynechococcus elongatus. FEBS J 273, 4913-4928 (2006).
19. T. Ishikawa, Y. Mizunoe, S. Kawabata, A. Takade, M. Harada, S. N. Wai, S. Yoshida: The iron-binding protein Dps confers hydrogen peroxide stress resistance to Campylobacter jejuni. J Bacteriol 185, 1010-1017 (2003). (Pubitemid 36139460)
20. F. Pacello, P. Ceci, S. Ammendola, P. Pasquali, E. Chiancone, A. Battistoni: Periplasmic Cu, Zn superoxide dismutase and cytoplasmic Dps concur in protecting Salmonella enterica serovar Typhimurium from extracellular reactive oxygen species. Biochim Biophys Acta 1780, 226-232 (2008).
21. J. Ueshima, M. Shoji, D. B. Ratnayake, K. Abe, S. Yoshida, K. Yamamoto, K. Nakayama: Purification, gene cloning, gene expression, and mutants of Dps from the obligate anaerobe Porphyromonas gingivalis. Infect Immun 71, 1170-1178 (2003). (Pubitemid 36254298)
22. T. A. Azam, S. Hiraga, A. Ishihama: Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells 5, 613-626 (2000). (Pubitemid 30641954)
23. D. Frenkiel-Krispin, S. Levin-Zaidman, E. Shimoni, S. G. Wolf, E. J. Wachtel, T. Arad, S. E. Finkel, R. Kolter, A. Minsky Regulated phase transitions of bacterial chromatin: a non-enzymatic pathway for generic DNA protection. EMBO J 20, 1184-1191 (2001). (Pubitemid 32186808)
24. P. Ceci, S. Cellai, E. Falvo, C. Rivetti, G. L. Rossi, E. Chiancone: DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus. Nucleic Acids Res 32, 5935- 5944 (2004). (Pubitemid 39619175)
25. S. G. Wolf, D. Frenkiel, T. Arad, S. E. Finkel, R. Kolter, A. Minsky: DNA protection by stress-induced biocrystallization. Nature 400, 83-85 (1999). (Pubitemid 29315116)
26. S. Roy, R. Saraswathi, D. Chatterji, M. Vijayan: Structural studies on the second Mycobacterium smegmatis Dps: invariant and variable features of structure, assembly and function. J Mol Biol 375, 948-959 (2008). (Pubitemid 350309389)
27. A. Grove, S. P. Wilkinson: Differential DNA binding and protection by dimeric and dodecameric forms of the ferritin homolog Dps from Deinococcus radiodurans. J Mol Biol 347, 495-508 (2005). (Pubitemid 40332360)
28. G. Bhattacharyya, A. Grove: The N-terminal extensions of Deinococcus radiodurans Dps-1 mediate DNA major groove interactions as well as assembly of the dodecamer. J Biol Chem 282, 11921-11930 (2007). (Pubitemid 47100660)
29. T. J. Stillman, M. Upadhyay, V. A. Norte, S. E. Sedelnikova, M. Carradus, S. Tzokov, P. A. Bullough, C. A. Shearman, M. J. Gasson, C. H. Williams, P. J. Artymiuk, J. Green: The crystal structures of Lactococcus lactis MG1363 Dps proteins reveal the presence of an Nterminal helix that is required for DNA binding. Mol Microbiol 57, 1101-1112 (2005). (Pubitemid 41139869)
30. S. Gupta, S. B. Pandit, N. Srinivasan, D. Chatterji: Proteomics analysis of carbon-starved Mycobacterium smegmatis: induction of Dps-like protein. Protein Eng 15, 503-512 (2002).
31. S. Gupta, D. Chatterji: Bimodal protection of DNA by Mycobacterium smegmatis DNA-binding protein from stationary phase cells. J Biol Chem 278, 5235-5241 (2003). (Pubitemid 36801036)
32. S. Roy, R. Saraswathi, S. Gupta, K. Sekar, D. Chatterji, M. Vijayan: Role of N and C-terminal tails in DNA binding and assembly in Dps: structural studies of Mycobacterium smegmatis Dps deletion mutants. J Mol Biol 370, 752-767 (2007). (Pubitemid 46879776)
33. P. Ceci, A. Ilari, E. Falvo, L. Giangiacomo, E. Chiancone: Reassessment of protein stability, DNA binding, and protection of Mycobacterium smegmatis Dps. J Biol Chem 280, 34776-3485 (2005).
34. P. Ceci, L. Mangiarotti, C. Rivetti, E. Chiancone: The neutrophil-activating Dps protein of Helicobacter pylori, HP-NAP, adopts a mechanism different from Escherichia coli Dps to bind and condense DNA. Nucleic Acids Res 35, 2247-2256 (2007). (Pubitemid 47073712)
35. M. Castruita, M. Saito, P. C. Schottel, L. A. Elmegreen, S. Myneni, E. I Stiefel, F. M. Morel: Overexpression and characterization of an iron storage and DNA-binding Dps protein from Trichodesmium erythraeum. Appl Environ Microbiol 72, 2918-2924 (2006).
36. M. Bozzi, G. Mignogna, S. Stefanini, D. Barra, C. Longhi, P. Valenti, E. Chiancone: A novel non-heme ironbinding ferritin related to the DNA-binding proteins of the Dps family in Listeria innocua. J Biol Chem 272, 3259- 3265 (1997).
37. E. Papinutto, W. G. Dundon, N. Pitulis, R. Battistutta, C. Montecucco, G. Zanotti: Structure of two iron-binding proteins from Bacillus anthracis. J Biol Chem 277, 15093- 15098 (2002). (Pubitemid 34952587)
38. K. Morikawa, R. L. Ohniwa, J. Kim, S. L. Takeshita, A. Maruyama, Y. Inose, K. Takeyasu, T. Ohta: Biochemical, molecular genetic, and structural analyses of the staphylococcal nucleoid. Microsc Microanal 13, 30-35 (2007). (Pubitemid 46457530)
39. R. L. Ohniwa, K. Morikawa, J. Kim, T. Ohta, A. Ishihama, C. Wada, K. Takeyasu: Dynamic state of DNA topology is essential for genome condensation in bacteria. EMBO J 25, 5591-5602 (2006). (Pubitemid 44847199)
40. R. Schneider, A. Travers, G. Muskhelishvili: FIS modulates growth phase-dependent topological transitions of DNA in Escherichia coli. Mol Microbiol 26, 519- 530 (1997). (Pubitemid 27487850)
41. R. Schneider, A. Travers, T. Kutateladze, G. Muskhelishvili: A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli. Mol Microbiol 34, 953-964 (1999). (Pubitemid 30000313)
42. D. Weinstein-Fischer, M. Elgrably-Weiss, S. Altuvia: Escherichia coli response to hydrogen peroxide: a role for DNA supercoiling, topoisomerase I and Fis. Mol Microbiol 35, 1413-1420 (2000). (Pubitemid 30175517)
43. S. Chodavarapu, R. Gomez, M. Vicente, J. M. Kaguni: Escherichia coli Dps interacts with DnaA protein to impede initiation: a model of adaptive mutation. Mol Microbiol 67, 1331-1346 (2008). (Pubitemid 351316958)
44. A. Ilari, S. Stefanini, E. Chiancone, D. Tsernoglou: The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site. Nat Struct Biol 7, 38- 43 (2000). (Pubitemid 30043246)
45. G. Zanotti, E. Papinutto, W. Dundon, R. Battistutta, M. Seveso, G. Giudice, R. Rappuoli, C. Montecucco. Structure of the neutrophil-activating protein from Helicobacter pylori. J Mol Biol 323, 125-130 (2002). (Pubitemid 35168485)