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Escherichia coli K-12 substr. MG1655 Protein: DNA polymerase III, β subunit



Gene: dnaN Accession Numbers: EG10242 (EcoCyc), b3701, ECK3693

Regulation Summary Diagram: ?

Component of: DNA polymerase III, holoenzyme (extended summary available)

Subunit composition of DNA polymerase III, β subunit = [DnaN]2

Summary:
The beta subunit of DNA polymerase III dimerizes to form the sliding clamp that links the core polymerase to DNA and allows processive DNA replication.

Beta binds 3' to an RNA primer at an ssDNA/duplex DNA junction in an ATP-dependent process catalyzed by the preinitiation complex [Maki88, Yao00]. The presence of beta stimulates DNA polymerase III activity, resulting in increased product length and processivity [LaDuca86]. The complete DNA polymerase III holoenzyme with both beta and ATP is at least twenty times more processive than core enzyme or holoenzyme lacking either of those components [Burgers82].

The beta clamp is very stable on DNA, requiring the ATP-dependent action of DNA polymerase III delta subunit for removal [Leu00]. Divalent magnesium is required for beta to maintain its dimer structure [Griep88]. On its own, the beta dimer diffuses bidirectionally on DNA in an ATP-independent fashion [Stukenberg91].

Beta binds to the core polymerase via the seven carboxy-terminal residues of the alpha subunit [Stukenberg91, Burnouf04]. Alpha interacts with the same portion of beta as the preinitiation protein delta, displacing delta and the preinitiation complex when it binds. Other polymerases (I, II, IV, V) also bind there as well [Lopez03]. Polymerase IV and the polymerase III core enzyme have been shown to compete for binding to beta [Burnouf04]. Beta is required for polymerase V-dependent translesion synthesis, but this uses a different interaction surface on beta than polymerase III [Sutton05]. Many proteins that bind beta have the consensus beta-binding motif QL(S/D)LF [Wijffels04].

A number of beta crystal structures have been evaluated. Based on a structure at 2.5 Å resolution, the beta dimer forms a ring with twelve internal α-helices, and each beta monomer has three identical domains [Kong92]. Crystal structures have also been determined at 1.9 and 1.85 A resolution [Oakley03]. A crystal structure of the interaction between beta and polymerase IV has also been determined [Burnouf04].

Beta is induced in an SOS-dependent manner following UV irradiation and exposure to an alkylating agent [Quinones89, Quillardet03]. Induction following UV exposure is posttranscriptional [Tadmor94]. UV irradiation has also been shown to induce synthesis of beta*, an in-frame isoform of beta that forms a homotrimer, can stimulate polymerase III activity and increases UV resistance [Skaliter96, PazElizur96, Skaliter96a]. Beta is also induced on entrance to stationary phase [Villarroya98].

The position of beta in the cell has been tracked. Beta exists in one or two condensed clusters in the nucleoid during normal growth and moves to the cell poles during replication [Onogi02].

dnaN has been the subject of a pilot study to screen for genetic interactions with null alleles in the Keio collection [Yong13].

Citations: [Burgers81, Johanson80]

Gene Citations: [PerezRoger91, Macian94]

Locations: cytosol

Map Position: [3,879,244 <- 3,880,344] (83.61 centisomes)
Length: 1101 bp / 366 aa

Molecular Weight of Polypeptide: 40.587 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0012098 , CGSC:842 , DIP:DIP-36038N , EchoBASE:EB0238 , EcoGene:EG10242 , EcoliWiki:b3701 , ModBase:P0A988 , OU-Microarray:b3701 , PortEco:dnaN , PR:PRO_000022466 , Pride:P0A988 , Protein Model Portal:P0A988 , RefSeq:NP_418156 , RegulonDB:EG10242 , SMR:P0A988 , String:511145.b3701 , UniProt:P0A988

Relationship Links: InterPro:IN-FAMILY:IPR001001 , InterPro:IN-FAMILY:IPR022634 , InterPro:IN-FAMILY:IPR022635 , InterPro:IN-FAMILY:IPR022637 , PDB:Structure:1JQJ , PDB:Structure:1JQL , PDB:Structure:1MMI , PDB:Structure:1OK7 , PDB:Structure:1UNN , PDB:Structure:1WAI , PDB:Structure:2POL , PDB:Structure:2XUR , PDB:Structure:3BEP , PDB:Structure:3D1E , PDB:Structure:3D1F , PDB:Structure:3D1G , PDB:Structure:3F1V , PDB:Structure:3PWE , PDB:Structure:3Q4J , PDB:Structure:3Q4K , PDB:Structure:3Q4L , PDB:Structure:3QSB , PDB:Structure:4K3K , PDB:Structure:4K3L , PDB:Structure:4K3M , PDB:Structure:4K3O , PDB:Structure:4K3P , PDB:Structure:4K3Q , PDB:Structure:4K3R , PDB:Structure:4K3S , PDB:Structure:4MJP , PDB:Structure:4MJQ , PDB:Structure:4MJR , Pfam:IN-FAMILY:PF00712 , Pfam:IN-FAMILY:PF02767 , Pfam:IN-FAMILY:PF02768 , Smart:IN-FAMILY:SM00480

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006271 - DNA strand elongation involved in DNA replication Inferred from experiment [LaDuca86]
GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0006260 - DNA replication Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Toste13, Jergic13, Bunting03, Kurz04, Kelman98, Naktinis95, Keyamura11, Stukenberg91, Parks09, Butland05, Jeruzalmi01a]
GO:0042802 - identical protein binding Inferred from experiment [Hauser14, Rajagopala14, Jergic13, Kong92, Lasserre06, Rajagopala09]
GO:0003677 - DNA binding Inferred by computational analysis [GOA01a]
GO:0003887 - DNA-directed DNA polymerase activity Inferred by computational analysis [UniProtGOA11a, GOA01, GOA01a]
GO:0008408 - 3'-5' exonuclease activity Inferred by computational analysis [GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016779 - nucleotidyltransferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0009360 - DNA polymerase III complex Inferred by computational analysis [GOA01a]

MultiFun Terms: information transfer DNA related DNA replication

Essentiality data for dnaN knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Subunit of: DNA polymerase III, holoenzyme

Subunit composition of DNA polymerase III, holoenzyme = [(DnaE)(DnaQ)(HolE)]3[(DnaX)3(HolB)(HolA)][(DnaN)2]2[(DnaX)2][(HolC)(HolD)]4
         DNA polymerase III, core enzyme = (DnaE)(DnaQ)(HolE) (summary available)
                 DNA polymerase III, α subunit = DnaE (extended summary available)
                 DNA polymerase III, ε subunit = DnaQ (extended summary available)
                 DNA polymerase III, θ subunit = HolE (extended summary available)
         DNA polymerase III, preinitiation complex = (DnaX)3(HolB)(HolA) (extended summary available)
                 DNA polymerase III, τ subunit = DnaX
                 DNA polymerase III, δ prime subunit = HolB (summary available)
                 DNA polymerase III, δ subunit = HolA (summary available)
         DNA polymerase III, β subunit = (DnaN)2 (extended summary available)
         DNA polymerase III, τ subunit dimer = (DnaX)2 (extended summary available)
                 DNA polymerase III, τ subunit = DnaX
         DNA polymerase III, ψ-χ subunit = (HolC)(HolD) (extended summary available)
                 DNA polymerase III, χ subunit = HolC
                 DNA polymerase III, ψ subunit = HolD

Summary:
DNA polymerase III holoenzyme is the enzyme primarily responsible for replicative DNA synthesis in E. coli. It carries out primer-initiated 5' to 3' polymerization of DNA on a single-stranded DNA template, as well as 3' to 5' exonucleolytic editing of mispaired nucleotides.

Replicative DNA polymerization begins when the preinitiation complex binds single-stranded DNA near an RNA primer. The preinitiation complex then loads the beta processivity clamp onto the DNA at this site, after which three core polymerases, chaperoned into place by the tau subunit, bind to the processivity clamp, with one polymerase on the leading strand and two on the lagging. DNA is synthesized 5' to 3' from primers on both the leading and lagging strands, covalently attaching the newly synthesized DNA to the primer. Tau displaces beta in the presence of duplex DNA, dissociating the polymerase from the template when it reaches a temporary stop on the lagging strand or when synthesis is complete on either strand [Maki88, Maki88a, Onrust95, Maki88b, Nusslein76, ReyesLamothe10].

For more detailed discussion of the stages of polymerase binding and DNA synthesis, see the individual entries for DNA polymerase III, preinitiation complex, DNA polymerase III, β subunit, DNA polymerase III, τ subunit dimer, DNA polymerase III, core enzyme and their constituent parts.

DNA polymerase III binds a region about 30 nucleotides long upstream of the RNA primer, with the alpha subunit making contact 9 nucleotides upstream and the beta clamp making contact 22 nucleotides upstream [Reems95, Reems94]. The preinitiation complex binds an area larger than this prior to being displaced by the core polymerase [Reems94]. In the presence of DNA polymerase III, RNA primer length is limited to 10 nucleotides, a limitation that is independent of the epsilon-mediated 3' to 5' exonuclease activity [Zechner92].

During polymerization, DNA polymerase III pauses at sites of potential secondary structure [LaDuca83]. The holoenzyme can traverse distances as long as 400 base pairs of duplex DNA to reach the next available 3' end and restart synthesis [ODonnell85]. Such jumps within the same template take 2 to 5 seconds, whereas transfer to a new template takes 30 seconds [Burgers83].

DNA polymerase III is required for several kinds of DNA repair, including some forms of double-strand break repair, fixing hydrogen-peroxide-induced damage and methyl-directed mismatch repair [Motamedi99, Hagensee89, Cooper93]. Mutations that inhibit polymerase III stimulate repeat expansion and lead to lower levels of unsaturation in fatty acids [Morag99, Suzuki98a].

UV mutagenesis and gap repair following UV damage to DNA both involve DNA polymerase III [CohenFix94, Tomer96]. The polymerase stalls at pyrimidine photodimers in vitro, but is capable of bypassing such lesions to continue synthesis [Shwartz87, Livneh86]. This bypass activity is stimulated by single-strand binding protein (SSB) but inhibited by the polymerase III beta subunit, which explains the relatively low rate of bypass in vivo [Shwartz87, Shavitt89].

Citations: [Cull95]

Credits:
Last-Curated ? 09-Jan-2006 by Shearer A , SRI International


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 1 -> 125
[UniProt10]
UniProt: I; Sequence Annotation Type: region of interest;
Mutagenesis-Variant 66
[Sutton04, UniProt13]
Alternate sequence: G → E; UniProt: In dnaN159; a temperature- and UV- sensitive mutation, displays altered DNA polymerase usage, chronically induced SOS response; when associated with A-174.
Protein-Segment 126 -> 253
[UniProt10]
UniProt: II; Sequence Annotation Type: region of interest;
Mutagenesis-Variant 174
[Sutton04, UniProt13]
Alternate sequence: G → A; UniProt: In dnaN159; a temperature- and UV- sensitive mutation, displays altered DNA polymerase usage, chronically induced SOS response; when associated with A-66.
Protein-Segment 254 -> 366
[UniProt10]
UniProt: III; Sequence Annotation Type: region of interest;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3701 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10242; confirmed by SwissProt match.


References

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

Bunting03: Bunting KA, Roe SM, Pearl LH (2003). "Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp." EMBO J 22(21);5883-92. PMID: 14592985

Burgers81: Burgers PM, Kornberg A, Sakakibara Y (1981). "The dnaN gene codes for the beta subunit of DNA polymerase III holoenzyme of escherichia coli." Proc Natl Acad Sci U S A 78(9);5391-5. PMID: 6458041

Burgers82: Burgers PM, Kornberg A (1982). "ATP activation of DNA polymerase III holoenzyme from Escherichia coli. II. Initiation complex: stoichiometry and reactivity." J Biol Chem 257(19);11474-8. PMID: 6749841

Burgers83: Burgers PM, Kornberg A (1983). "The cycling of Escherichia coli DNA polymerase III holoenzyme in replication." J Biol Chem 258(12);7669-75. PMID: 6345527

Burnouf04: Burnouf DY, Olieric V, Wagner J, Fujii S, Reinbolt J, Fuchs RP, Dumas P (2004). "Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases." J Mol Biol 335(5);1187-97. PMID: 14729336

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

CohenFix94: Cohen-Fix O, Livneh Z (1994). "In vitro UV mutagenesis associated with nucleotide excision-repair gaps in Escherichia coli." J Biol Chem 269(7);4953-8. PMID: 8106470

Cooper93: Cooper DL, Lahue RS, Modrich P (1993). "Methyl-directed mismatch repair is bidirectional." J Biol Chem 268(16);11823-9. PMID: 8389365

Cull95: Cull MG, McHenry CS (1995). "Purification of Escherichia coli DNA polymerase III holoenzyme." Methods Enzymol 262;22-35. PMID: 8594350

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

Griep88: Griep MA, McHenry CS (1988). "The dimer of the beta subunit of Escherichia coli DNA polymerase III holoenzyme is dissociated into monomers upon binding magnesium(II)." Biochemistry 27(14);5210-5. PMID: 3048397

Hagensee89: Hagensee ME, Moses RE (1989). "Multiple pathways for repair of hydrogen peroxide-induced DNA damage in Escherichia coli." J Bacteriol 171(2);991-5. PMID: 2644241

Hauser14: Hauser R, Ceol A, Rajagopala SV, Mosca R, Siszler G, Wermke N, Sikorski P, Schwarz F, Schick M, Wuchty S, Aloy P, Uetz P (2014). "A Second-generation Protein-Protein Interaction Network of Helicobacter pylori." Mol Cell Proteomics 13(5);1318-29. PMID: 24627523

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Jergic13: Jergic S, Horan NP, Elshenawy MM, Mason CE, Urathamakul T, Ozawa K, Robinson A, Goudsmits JM, Wang Y, Pan X, Beck JL, van Oijen AM, Huber T, Hamdan SM, Dixon NE (2013). "A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode." EMBO J 32(9);1322-33. PMID: 23435564

Jeruzalmi01a: Jeruzalmi D, Yurieva O, Zhao Y, Young M, Stewart J, Hingorani M, O'Donnell M, Kuriyan J (2001). "Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. coli DNA polymerase III." Cell 106(4);417-28. PMID: 11525728

Johanson80: Johanson KO, McHenry CS (1980). "Purification and characterization of the beta subunit of the DNA polymerase III holoenzyme of Escherichia coli." J Biol Chem 255(22);10984-90. PMID: 6776124

Kelman98: Kelman Z, Yuzhakov A, Andjelkovic J, O'Donnell M (1998). "Devoted to the lagging strand-the subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly." EMBO J 17(8);2436-49. PMID: 9545254

Keyamura11: Keyamura K, Katayama T (2011). "DnaA protein DNA-binding domain binds to Hda protein to promote inter-AAA+ domain interaction involved in regulatory inactivation of DnaA." J Biol Chem 286(33);29336-46. PMID: 21708944

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Kong92: Kong XP, Onrust R, O'Donnell M, Kuriyan J (1992). "Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp." Cell 69(3);425-37. PMID: 1349852

Kurz04: Kurz M, Dalrymple B, Wijffels G, Kongsuwan K (2004). "Interaction of the sliding clamp beta-subunit and Hda, a DnaA-related protein." J Bacteriol 186(11);3508-15. PMID: 15150238

LaDuca83: LaDuca RJ, Fay PJ, Chuang C, McHenry CS, Bambara RA (1983). "Site-specific pausing of deoxyribonucleic acid synthesis catalyzed by four forms of Escherichia coli DNA polymerase III." Biochemistry 22(22);5177-88. PMID: 6360204

LaDuca86: LaDuca RJ, Crute JJ, McHenry CS, Bambara RA (1986). "The beta subunit of the Escherichia coli DNA polymerase III holoenzyme interacts functionally with the catalytic core in the absence of other subunits." J Biol Chem 261(16);7550-7. PMID: 3519609

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

Leu00: Leu FP, Hingorani MM, Turner J, O'Donnell M (2000). "The delta subunit of DNA polymerase III holoenzyme serves as a sliding clamp unloader in Escherichia coli." J Biol Chem 275(44);34609-18. PMID: 10924523

Livneh86: Livneh Z (1986). "Mechanism of replication of ultraviolet-irradiated single-stranded DNA by DNA polymerase III holoenzyme of Escherichia coli. Implications for SOS mutagenesis." J Biol Chem 261(20);9526-33. PMID: 2941423

Lopez03: Lopez de Saro FJ, Georgescu RE, Goodman MF, O'Donnell M (2003). "Competitive processivity-clamp usage by DNA polymerases during DNA replication and repair." EMBO J 22(23);6408-18. PMID: 14633999

Macian94: Macian F, Perez-Roger I, Armengod ME (1994). "An improved vector system for constructing transcriptional lacZ fusions: analysis of regulation of the dnaA, dnaN, recF and gyrB genes of Escherichia coli." Gene 1994;145(1);17-24. PMID: 8045420

Maki88: Maki S, Kornberg A (1988). "DNA polymerase III holoenzyme of Escherichia coli. III. Distinctive processive polymerases reconstituted from purified subunits." J Biol Chem 263(14);6561-9. PMID: 3283127

Maki88a: Maki S, Kornberg A (1988). "DNA polymerase III holoenzyme of Escherichia coli. II. A novel complex including the gamma subunit essential for processive synthesis." J Biol Chem 263(14);6555-60. PMID: 3283126

Maki88b: Maki H, Maki S, Kornberg A (1988). "DNA Polymerase III holoenzyme of Escherichia coli. IV. The holoenzyme is an asymmetric dimer with twin active sites." J Biol Chem 263(14);6570-8. PMID: 3283128

Morag99: Morag AS, Saveson CJ, Lovett ST (1999). "Expansion of DNA repeats in Escherichia coli: effects of recombination and replication functions." J Mol Biol 289(1);21-7. PMID: 10339402

Motamedi99: Motamedi MR, Szigety SK, Rosenberg SM (1999). "Double-strand-break repair recombination in Escherichia coli: physical evidence for a DNA replication mechanism in vivo." Genes Dev 13(21);2889-903. PMID: 10557215

Naktinis95: Naktinis V, Onrust R, Fang L, O'Donnell M (1995). "Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. II. Intermediate complex between the clamp loader and its clamp." J Biol Chem 270(22);13358-65. PMID: 7768937

Nusslein76: Nusslein V, Henke S, Johnston LH (1976). "Replication of E. coli duplex DNA in vitro. The separation of the DNA containing fractions of a lysate from the soluble enzymes and their complementation properties." Mol Gen Genet 145(2);183-90. PMID: 778584

Oakley03: Oakley AJ, Prosselkov P, Wijffels G, Beck JL, Wilce MC, Dixon NE (2003). "Flexibility revealed by the 1.85 A crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III." Acta Crystallogr D Biol Crystallogr 59(Pt 7);1192-9. PMID: 12832762

ODonnell85: O'Donnell ME, Kornberg A (1985). "Dynamics of DNA polymerase III holoenzyme of Escherichia coli in replication of a multiprimed template." J Biol Chem 260(23);12875-83. PMID: 2413035

Onogi02: Onogi T, Ohsumi K, Katayama T, Hiraga S (2002). "Replication-dependent recruitment of the beta-subunit of DNA polymerase III from cytosolic spaces to replication forks in Escherichia coli." J Bacteriol 184(3);867-70. PMID: 11790763

Onrust95: Onrust R, Finkelstein J, Turner J, Naktinis V, O'Donnell M (1995). "Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. III. Interface between two polymerases and the clamp loader." J Biol Chem 270(22);13366-77. PMID: 7768938

Parks09: Parks AR, Li Z, Shi Q, Owens RM, Jin MM, Peters JE (2009). "Transposition into replicating DNA occurs through interaction with the processivity factor." Cell 138(4);685-95. PMID: 19703395

PazElizur96: Paz-Elizur T, Skaliter R, Blumenstein S, Livneh Z (1996). "Beta*, a UV-inducible smaller form of the beta subunit sliding clamp of DNA polymerase III of Escherichia coli. I. Gene expression and regulation." J Biol Chem 271(5);2482-90. PMID: 8576211

PerezRoger91: Perez-Roger I, Garcia-Sogo M, Navarro-Avino JP, Lopez-Acedo C, Macian F, Armengod ME (1991). "Positive and negative regulatory elements in the dnaA-dnaN-recF operon of Escherichia coli." Biochimie 73(2-3);329-34. PMID: 1883890

Quillardet03: Quillardet P, Rouffaud MA, Bouige P (2003). "DNA array analysis of gene expression in response to UV irradiation in Escherichia coli." Res Microbiol 154(8);559-72. PMID: 14527657

Quinones89: Quinones A, Kaasch J, Kaasch M, Messer W (1989). "Induction of dnaN and dnaQ gene expression in Escherichia coli by alkylation damage to DNA." EMBO J 8(2);587-93. PMID: 2656258

Rajagopala09: Rajagopala SV, Hughes KT, Uetz P (2009). "Benchmarking yeast two-hybrid systems using the interactions of bacterial motility proteins." Proteomics 9(23);5296-302. PMID: 19834901

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Reems94: Reems JA, McHenry CS (1994). "Escherichia coli DNA polymerase III holoenzyme footprints three helical turns of its primer." J Biol Chem 269(52);33091-6. PMID: 7806536

Reems95: Reems JA, Wood S, McHenry CS (1995). "Escherichia coli DNA polymerase III holoenzyme subunits alpha, beta, and gamma directly contact the primer-template." J Biol Chem 270(10);5606-13. PMID: 7890680

ReyesLamothe10: Reyes-Lamothe R, Sherratt DJ, Leake MC (2010). "Stoichiometry and architecture of active DNA replication machinery in Escherichia coli." Science 328(5977);498-501. PMID: 20413500

Shavitt89: Shavitt O, Livneh Z (1989). "The beta subunit modulates bypass and termination at UV lesions during in vitro replication with DNA polymerase III holoenzyme of Escherichia coli." J Biol Chem 264(19);11275-81. PMID: 2661556

Shwartz87: Shwartz H, Livneh Z (1987). "Dynamics of termination during in vitro replication of ultraviolet-irradiated DNA with DNA polymerase III holoenzyme of Escherichia coli." J Biol Chem 262(22);10518-23. PMID: 2956258

Skaliter96: Skaliter R, Bergstein M, Livneh Z (1996). "Beta*, a UV-inducible shorter form of the beta subunit of DNA polymerase III of Escherichia coli. II. Overproduction, purification, and activity as a polymerase processivity clamp." J Biol Chem 271(5);2491-6. PMID: 8576212

Skaliter96a: Skaliter R, Paz-Elizur T, Livneh Z (1996). "A smaller form of the sliding clamp subunit of DNA polymerase III is induced by UV irradiation in Escherichia coli." J Biol Chem 271(5);2478-81. PMID: 8576210

Stukenberg91: Stukenberg PT, Studwell-Vaughan PS, O'Donnell M (1991). "Mechanism of the sliding beta-clamp of DNA polymerase III holoenzyme." J Biol Chem 266(17);11328-34. PMID: 2040637

Sutton04: Sutton MD (2004). "The Escherichia coli dnaN159 mutant displays altered DNA polymerase usage and chronic SOS induction." J Bacteriol 186(20);6738-48. PMID: 15466025

Sutton05: Sutton MD, Duzen JM, Maul RW (2005). "Mutant forms of the Escherichia colibeta sliding clamp that distinguish between its roles in replication and DNA polymerase V-dependent translesion DNA synthesis." Mol Microbiol 55(6);1751-66. PMID: 15752198

Suzuki98a: Suzuki E, Kondo T, Makise M, Mima S, Sakamoto K, Tsuchiya T, Mizushima T (1998). "Alteration in levels of unsaturated fatty acids in mutants of Escherichia coli defective in DNA replication." Biol Pharm Bull 21(7);657-61. PMID: 9703244

Tadmor94: Tadmor Y, Bergstein M, Skaliter R, Shwartz H, Livneh Z (1994). "Beta subunit of DNA polymerase III holoenzyme is induced upon ultraviolet irradiation or nalidixic acid treatment of Escherichia coli." Mutat Res 308(1);53-64. PMID: 7516486

Tomer96: Tomer G, Cohen-Fix O, O'Donnell M, Goodman M, Livneh Z (1996). "Reconstitution of repair-gap UV mutagenesis with purified proteins from Escherichia coli: a role for DNA polymerases III and II." Proc Natl Acad Sci U S A 93(4);1376-80. PMID: 8643639

Toste13: Toste Rego A, Holding AN, Kent H, Lamers MH (2013). "Architecture of the Pol III-clamp-exonuclease complex reveals key roles of the exonuclease subunit in processive DNA synthesis and repair." EMBO J 32(9);1334-43. PMID: 23549287

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 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."

Villarroya98: Villarroya M, Perez-Roger I, Macian F, Armengod ME (1998). "Stationary phase induction of dnaN and recF, two genes of Escherichia coli involved in DNA replication and repair." EMBO J 17(6);1829-37. PMID: 9501104

Wijffels04: Wijffels G, Dalrymple BP, Prosselkov P, Kongsuwan K, Epa VC, Lilley PE, Jergic S, Buchardt J, Brown SE, Alewood PF, Jennings PA, Dixon NE (2004). "Inhibition of protein interactions with the beta 2 sliding clamp of Escherichia coli DNA polymerase III by peptides from beta 2-binding proteins." Biochemistry 43(19);5661-71. PMID: 15134440

Yao00: Yao N, Leu FP, Anjelkovic J, Turner J, O'Donnell M (2000). "DNA structure requirements for the Escherichia coli gamma complex clamp loader and DNA polymerase III holoenzyme." J Biol Chem 275(15);11440-50. PMID: 10753961

Yong13: Yong HT, Yamamoto N, Takeuchi R, Hsieh YJ, Conrad TM, Datsenko KA, Nakayashiki T, Wanner BL, Mori H (2013). "Development of a system for discovery of genetic interactions for essential genes in Escherichia coli K-12." Genes Genet Syst 88(4);233-40. PMID: 24463526

Zechner92: Zechner EL, Wu CA, Marians KJ (1992). "Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. III. A polymerase-primase interaction governs primer size." J Biol Chem 267(6);4054-63. PMID: 1531480

Other References Related to Gene Regulation

Armengod88: Armengod ME, Garcia-Sogo M, Lambies E (1988). "Transcriptional organization of the dnaN and recF genes of Escherichia coli K-12." J Biol Chem 1988;263(24);12109-14. PMID: 2841344

Hansen82: Hansen FG, Hansen EB, Atlung T (1982). "The nucleotide sequence of the dnaA gene promoter and of the adjacent rpmH gene, coding for the ribosomal protein L34, of Escherichia coli." EMBO J 1982;1(9);1043-8. PMID: 6329723

Lee96: Lee YS, Kim H, Hwang DS (1996). "Transcriptional activation of the dnaA gene encoding the initiator for oriC replication by IciA protein, an inhibitor of in vitro oriC replication in Escherichia coli." Mol Microbiol 1996;19(2);389-96. PMID: 8825783

Lee97: Lee YS, Hwang DS (1997). "Occlusion of RNA polymerase by oligomerization of DnaA protein over the dnaA promoter of Escherichia coli." J Biol Chem 272(1);83-8. PMID: 8995231

Lee97a: Lee Y, Lee H, Yim J, Hwang D (1997). "The binding of two dimers of IciA protein to the dnaA promoter 1P element enhances the binding of RNA polymerase to the dnaA promoter 1P." Nucleic Acids Res 1997;25(17);3486-9. PMID: 9254708

Marbaniang11: Marbaniang CN, Gowrishankar J (2011). "Role of ArgP (IciA) in Lysine-Mediated Repression in Escherichia coli." J Bacteriol 193(21);5985-96. PMID: 21890697

Ohmori84: Ohmori H, Kimura M, Nagata T, Sakakibara Y (1984). "Structural analysis of the dnaA and dnaN genes of Escherichia coli." Gene 1984;28(2);159-70. PMID: 6234204

Saggioro13: Saggioro C, Olliver A, Sclavi B (2013). "Temperature-dependence of the DnaA-DNA interaction and its effect on the autoregulation of dnaA expression." Biochem J 449(2);333-41. PMID: 23092251


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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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