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Escherichia coli K-12 substr. MG1655 Protein: Dps complex; stationary phase nucleoid component that sequesters iron and protects DNA from damage



Gene: dps Accession Numbers: EG11415 (EcoCyc), b0812, ECK0801

Synonyms: pexB, vtm

Regulation Summary Diagram: ?

Subunit composition of Dps complex; stationary phase nucleoid component that sequesters iron and protects DNA from damage = [Dps]12
         stationary phase nucleoid protein that sequesters iron and protects DNA from damage = Dps

Summary:
Dps is a highly abundant protein in stationary-phase E. coli and is required for the normal starvation response [Almiron92] and long-term stationary phase viability [Nair04a]. The protein was shown to be involved in protection from multiple stresses, including oxidative stress caused by treatment with hypochlorous acid [Dukan96] or hydrogen peroxide [Dukan96, Martinez97a], the stress of exposure to visible light in a seawater environment [Gourmelon97] or under conditions of fatty acid starvation [Gong02a], and N-ethylmaleimide (NEM) treatment [Ferguson98b].

Dps binds tightly to DNA in a non-sequence-specific manner [Almiron92, Azam99], forming a DNA-protein crystal [Wolf99] that protects the DNA from damage [Martinez97a]. Dps is the major nucleoid protein at stationary phase [Ali99], showing evenly distributed localization within the nucleoid [Azam00]. At the onset of stationary phase, Dps is involved in restructuring chromatin into ordered toroidal structures [FrenkielKrispin04, Kim04g].

Dps forms a ferritin-like, hollow, 12-subunit homo-oligomeric complex [Grant98a]. Dps collects iron, which serves as a reducing agent in oxidative damage protection/repair [Rychlewski99, Zhao02b]. Iron acquisition by Dps has been characterized in detail [Zhao02b, Ilari02a].

Dps is phosphorylated in a wall-less L-form E. coli strain [Freestone98].

A crystal structure is presented at 1.6 Å resolution [Grant98a].

Regulation has been described [Altuvia94, Ivanova97, Rockabrand98, Michan99, Bechtloff99, Ali99, Jurgen00, Phadtare01, Eppler02, Weichart03]. Dps is induced by starvation [Almiron92]. Starvation of carbon or oxidative stress cause transcriptional induction, and starvation of nitrogen causes post-transcriptional induction [Lomovskaya94]. Dps abundance is subject to regulation by proteolysis [Stephani03]. The polyadenylation of dps mRNA has been examined [Cao97a].

Reviews: [Ishihama99, Andrews03, Chiancone10, Calhoun11, Zeth12]

Citations: [Gerard99, FrenkielKrispin01]

Gene Citations: [Suzuki97a]

Locations: cytosol, bacterial nucleoid, membrane

Map Position: [847,631 <- 848,134] (18.27 centisomes)
Length: 504 bp / 167 aa

Molecular Weight of Polypeptide: 18.695 kD (from nucleotide sequence), 18 kD (experimental), 19 kD (experimental)

Unification Links: ASAP:ABE-0002776 , CGSC:31650 , DIP:DIP-35919N , EchoBASE:EB1387 , EcoGene:EG11415 , EcoliWiki:b0812 , Mint:MINT-1220368 , ModBase:P0ABT2 , OU-Microarray:b0812 , PortEco:dps , PR:PRO_000022478 , Pride:P0ABT2 , Protein Model Portal:P0ABT2 , RefSeq:NP_415333 , RegulonDB:EG11415 , SMR:P0ABT2 , String:511145.b0812 , UniProt:P0ABT2

Relationship Links: InterPro:IN-FAMILY:IPR002177 , InterPro:IN-FAMILY:IPR008331 , InterPro:IN-FAMILY:IPR009078 , InterPro:IN-FAMILY:IPR012347 , InterPro:IN-FAMILY:IPR023067 , InterPro:IN-FAMILY:IPR023188 , PDB:Structure:1DPS , PDB:Structure:1F30 , PDB:Structure:1F33 , PDB:Structure:1JRE , PDB:Structure:1JTS , PDB:Structure:1L8H , PDB:Structure:1L8I , PDB:Structure:2W9R , PDB:Structure:3O2H , Pfam:IN-FAMILY:PF00210 , Prints:IN-FAMILY:PR01346 , Prosite:IN-FAMILY:PS00818 , Prosite:IN-FAMILY:PS00819

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0042594 - response to starvation Inferred from experiment [Almiron92]
GO:0006879 - cellular iron ion homeostasis Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0006950 - response to stress Inferred by computational analysis [GOA01a]
GO:0030261 - chromosome condensation Inferred by computational analysis [UniProtGOA11a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, Almiron92, Azam99]
GO:0005515 - protein binding Inferred from experiment [Ninnis09, Schuenemann09, Schmidt09, Chodavarapu08]
GO:0008199 - ferric iron binding Inferred by computational analysis [GOA06, GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0016722 - oxidoreductase activity, oxidizing metal ions Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0005829 - cytosol
GO:0009295 - nucleoid Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell processes adaptations starvation
information transfer protein related nucleoproteins, basic proteins
metabolism central intermediary metabolism incorporation of metal ions

Essentiality data for dps knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Noll98, Altuvia94, Foster93, Link97, UniProt11a]
UniProt: Removed.
Chain 2 -> 167
[UniProt09]
UniProt: DNA protection during starvation protein;
Sequence-Conflict 18
[Altuvia94, UniProt10a]
Alternate sequence: R → N; UniProt: (in Ref. 8; AA sequence);
Metal-Binding-Site 51
[UniProt10a]
UniProt: Iron 1; shared with dodecameric partner;
Sequence-Conflict 68
[Lomovskaya94, UniProt10a]
Alternate sequence: G → A; UniProt: (in Ref. 2; AAA21855);
Metal-Binding-Site 78
[UniProt10a]
UniProt: Iron 1;
Metal-Binding-Site 82
[UniProt10a]
UniProt: Iron 1;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0812 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11415; confirmed by SwissProt match.


References

Ali99: Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A (1999). "Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid." J Bacteriol 181(20);6361-70. PMID: 10515926

Almiron92: Almiron M, Link AJ, Furlong D, Kolter R (1992). "A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli." Genes Dev 1992;6(12B);2646-54. PMID: 1340475

Altuvia94: Altuvia S, Almiron M, Huisman G, Kolter R, Storz G (1994). "The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase." Mol Microbiol 1994;13(2);265-72. PMID: 7984106

Andrews03: Andrews SC, Robinson AK, Rodriguez-Quinones F (2003). "Bacterial iron homeostasis." FEMS Microbiol Rev 27(2-3);215-37. PMID: 12829269

Azam00: Azam TA, Hiraga S, Ishihama A (2000). "Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid." Genes Cells 5(8);613-26. PMID: 10947847

Azam99: Azam TA, Ishihama A (1999). "Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity." J Biol Chem 274(46);33105-13. PMID: 10551881

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bechtloff99: Bechtloff D, Grunenfelder B, Akerlund T, Nordstrom K (1999). "Analysis of protein synthesis rates after initiation of chromosome replication in Escherichia coli." J Bacteriol 181(20);6292-9. PMID: 10515917

Calhoun11: Calhoun LN, Kwon YM (2011). "Structure, function and regulation of the DNA-binding protein Dps and its role in acid and oxidative stress resistance in Escherichia coli: a review." J Appl Microbiol 110(2);375-86. PMID: 21143355

Cao97a: Cao GJ, Sarkar N (1997). "Stationary phase-specific mRNAs in Escherichia coli are polyadenylated." Biochem Biophys Res Commun 239(1);46-50. PMID: 9345267

Chiancone10: Chiancone E, Ceci P (2010). "The multifaceted capacity of Dps proteins to combat bacterial stress conditions: Detoxification of iron and hydrogen peroxide and DNA binding." Biochim Biophys Acta 1800(8);798-805. PMID: 20138126

Chodavarapu08: Chodavarapu S, Gomez R, Vicente M, Kaguni JM (2008). "Escherichia coli Dps interacts with DnaA protein to impede initiation: a model of adaptive mutation." Mol Microbiol 67(6);1331-46. PMID: 18284581

Dukan96: Dukan S, Touati D (1996). "Hypochlorous acid stress in Escherichia coli: resistance, DNA damage, and comparison with hydrogen peroxide stress." J Bacteriol 178(21);6145-50. PMID: 8892812

Eppler02: Eppler T, Postma P, Schutz A, Volker U, Boos W (2002). "Glycerol-3-phosphate-induced catabolite repression in Escherichia coli." J Bacteriol 184(11);3044-52. PMID: 12003946

Ferguson98b: Ferguson GP, Creighton RI, Nikolaev Y, Booth IR (1998). "Importance of RpoS and Dps in survival of exposure of both exponential- and stationary-phase Escherichia coli cells to the electrophile N-ethylmaleimide." J Bacteriol 180(5);1030-6. PMID: 9495739

Foster93: Foster SJ (1993). "Purification and characterization of an 'actomyosin' complex from Escherichia coli W3110." FEMS Microbiol Lett 110(3);295-8. PMID: 8354462

Freestone98: Freestone P, Grant S, Trinei M, Onoda T, Norris V (1998). "Protein phosphorylation in Escherichia coli L. form NC-7." Microbiology 144 ( Pt 12);3289-95. PMID: 9884220

FrenkielKrispin01: Frenkiel-Krispin D, Levin-Zaidman S, Shimoni E, Wolf SG, Wachtel EJ, Arad T, Finkel SE, Kolter R, Minsky A (2001). "Regulated phase transitions of bacterial chromatin: a non-enzymatic pathway for generic DNA protection." EMBO J 20(5);1184-91. PMID: 11230141

FrenkielKrispin04: Frenkiel-Krispin D, Ben-Avraham I, Englander J, Shimoni E, Wolf SG, Minsky A (2004). "Nucleoid restructuring in stationary-state bacteria." Mol Microbiol 51(2);395-405. PMID: 14756781

Gerard99: Gerard F, Dri AM, Moreau PL (1999). "Role of Escherichia coli RpoS, LexA and H-NS global regulators in metabolism and survival under aerobic, phosphate-starvation conditions." Microbiology 145 ( Pt 7);1547-62. PMID: 10439394

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Gong02a: Gong L, Takayama K, Kjelleberg S (2002). "Role of spoT-dependent ppGpp accumulation in the survival of light-exposed starved bacteria." Microbiology 148(Pt 2);559-70. PMID: 11832519

Gourmelon97: Gourmelon M, Touati D, Pommepuy M, Cormier M (1997). "Survival of Escherichia coli exposed to visible light in seawater: analysis of rpoS-dependent effects." Can J Microbiol 43(11);1036-43. PMID: 9436305

Grant98a: Grant RA, Filman DJ, Finkel SE, Kolter R, Hogle JM (1998). "The crystal structure of Dps, a ferritin homolog that binds and protects DNA." Nat Struct Biol 5(4);294-303. PMID: 9546221

Ilari02a: Ilari A, Ceci P, Ferrari D, Rossi GL, Chiancone E (2002). "Iron incorporation into Escherichia coli Dps gives rise to a ferritin-like microcrystalline core." J Biol Chem 277(40);37619-23. PMID: 12163499

Ishihama99: Ishihama A (1999). "Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival." Genes Cells 4(3);135-43. PMID: 10320479

Ivanova97: Ivanova AB, Glinsky GV, Eisenstark A (1997). "Role of rpoS regulon in resistance to oxidative stress and near-UV radiation in delta oxyR suppressor mutants of Escherichia coli." Free Radic Biol Med 23(4);627-36. PMID: 9215808

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Jurgen00: Jurgen B, Lin HY, Riemschneider S, Scharf C, Neubauer P, Schmid R, Hecker M, Schweder T (2000). "Monitoring of genes that respond to overproduction of an insoluble recombinant protein in Escherichia coli glucose-limited fed-batch fermentations." Biotechnol Bioeng 70(2);217-24. PMID: 10972933

Kim04g: Kim J, Yoshimura SH, Hizume K, Ohniwa RL, Ishihama A, Takeyasu K (2004). "Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy." Nucleic Acids Res 32(6);1982-92. PMID: 15060178

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

Lomovskaya94: Lomovskaya OL, Kidwell JP, Matin A (1994). "Characterization of the sigma 38-dependent expression of a core Escherichia coli starvation gene, pexB." J Bacteriol 176(13);3928-35. PMID: 8021175

Martinez97a: Martinez A, Kolter R (1997). "Protection of DNA during oxidative stress by the nonspecific DNA-binding protein Dps." J Bacteriol 179(16);5188-94. PMID: 9260963

Michan99: Michan C, Manchado M, Dorado G, Pueyo C (1999). "In vivo transcription of the Escherichia coli oxyR regulon as a function of growth phase and in response to oxidative stress." J Bacteriol 181(9);2759-64. PMID: 10217765

Nair04a: Nair S, Finkel SE (2004). "Dps protects cells against multiple stresses during stationary phase." J Bacteriol 186(13);4192-8. PMID: 15205421

Ninnis09: Ninnis RL, Spall SK, Talbo GH, Truscott KN, Dougan DA (2009). "Modification of PATase by L/F-transferase generates a ClpS-dependent N-end rule substrate in Escherichia coli." EMBO J 28(12);1732-44. PMID: 19440203

Noll98: Noll M, Petrukhin K, Lutsenko S (1998). "Identification of a novel transcription regulator from Proteus mirabilis, PMTR, revealed a possible role of YJAI protein in balancing zinc in Escherichia coli." J Biol Chem 273(33);21393-401. PMID: 9694902

Phadtare01: Phadtare S, Inouye M (2001). "Role of CspC and CspE in regulation of expression of RpoS and UspA, the stress response proteins in Escherichia coli." J Bacteriol 183(4);1205-14. PMID: 11157932

Rockabrand98: Rockabrand D, Livers K, Austin T, Kaiser R, Jensen D, Burgess R, Blum P (1998). "Roles of DnaK and RpoS in starvation-induced thermotolerance of Escherichia coli." J Bacteriol 180(4);846-54. PMID: 9473038

Rychlewski99: Rychlewski L, Zhang B, Godzik A (1999). "Functional insights from structural predictions: analysis of the Escherichia coli genome." Protein Sci 8(3);614-24. PMID: 10091664

Schmidt09: Schmidt R, Zahn R, Bukau B, Mogk A (2009). "ClpS is the recognition component for Escherichia coli substrates of the N-end rule degradation pathway." Mol Microbiol 72(2);506-17. PMID: 19317833

Schuenemann09: Schuenemann VJ, Kralik SM, Albrecht R, Spall SK, Truscott KN, Dougan DA, Zeth K (2009). "Structural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS." EMBO Rep 10(5);508-14. PMID: 19373253

Stephani03: Stephani K, Weichart D, Hengge R (2003). "Dynamic control of Dps protein levels by ClpXP and ClpAP proteases in Escherichia coli." Mol Microbiol 49(6);1605-14. PMID: 12950924

Suzuki97a: Suzuki K, Okada K, Kamiya Y, Zhu XF, Nakagawa T, Kawamukai M, Matsuda H (1997). "Analysis of the decaprenyl diphosphate synthase (dps) gene in fission yeast suggests a role of ubiquinone as an antioxidant." J Biochem 121(3);496-505. PMID: 9133618

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Weichart03: Weichart D, Querfurth N, Dreger M, Hengge-Aronis R (2003). "Global role for ClpP-containing proteases in stationary-phase adaptation of Escherichia coli." J Bacteriol 185(1);115-25. PMID: 12486047

Wolf99: Wolf SG, Frenkiel D, Arad T, Finkel SE, Kolter R, Minsky A (1999). "DNA protection by stress-induced biocrystallization." Nature 400(6739);83-5. PMID: 10403254

Zeth12: Zeth K (2012). "Dps biomineralizing proteins: multifunctional architects of nature." Biochem J 445(3);297-311. PMID: 22788214

Zhao02b: Zhao G, Ceci P, Ilari A, Giangiacomo L, Laue TM, Chiancone E, Chasteen ND (2002). "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(31);27689-96. PMID: 12016214

Other References Related to Gene Regulation

Baez13: Baez A, Shiloach J (2013). "Escherichia coli avoids high dissolved oxygen stress by activation of SoxRS and manganese-superoxide dismutase." Microb Cell Fact 12;23. PMID: 23497217

Campos07: Campos E, Montella C, Garces F, Baldoma L, Aguilar J, Badia J (2007). "Aerobic L-ascorbate metabolism and associated oxidative stress in Escherichia coli." Microbiology 153(Pt 10);3399-408. PMID: 17906139

Grainger08: Grainger DC, Goldberg MD, Lee DJ, Busby SJ (2008). "Selective repression by Fis and H-NS at the Escherichia coli dps promoter." Mol Microbiol 68(6);1366-77. PMID: 18452510

Lacour04: Lacour S, Landini P (2004). "SigmaS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of sigmaS-dependent genes and identification of their promoter sequences." J Bacteriol 186(21);7186-95. PMID: 15489429

Yamamoto11a: Yamamoto K, Ishihama A, Busby SJ, Grainger DC (2011). "The Escherichia coli K-12 MntR Miniregulon Includes dps, Which Encodes the Major Stationary-Phase DNA-Binding Protein." J Bacteriol 193(6);1477-80. PMID: 21239586


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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