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Escherichia coli K-12 substr. MG1655 Protein: primosomal replication protein N



Gene: priB Accession Numbers: EG10764 (EcoCyc), b4201, ECK4197

Regulation Summary Diagram: ?

Component of: primosome (summary available)

Subunit composition of primosomal replication protein N = [PriB]2

Summary:
PriB is a component of the primosome, a multiprotein complex that is believed to be involved in restart of stalled replication forks. Based on genetic studies, some PriA-dependent restart pathways require PriB [Sandler00]. Other research shows that a pathway dependent on both PriA and PriB is used when stalled replication forks have no leading strand gaps, alternately turning to a PriC pathway when there are large gaps [Heller05].

PriB is a core component of the primosome, binding to PriA and single-stranded DNA (ssDNA) shortly after PriA binds DNA, stabilizing the PriA-DNA interaction [Ng96, Allen93]. PriB also assists in subsequent binding of DnaT to PriA [Liu96c]. In the case of phiX174 phage, PriB interacts directly with single-strand binding protein (SSB) [Low82]. While it is bound, PriB stimulates the helicase activity and processivity of PriA [Cadman05].

Several crystal structures have been determined for PriB, all to around 2 Å resolution. Based on these structures, PriB exists as a dimer and is very structurally similar to SSB [Shioi05, Lopper04, Liu04a]. Based on sequence comparison and operon organization PriB appears to have evolved from SSB via gene duplication [Ponomarev03]. A 2.7 Å-resolution crystal structure of PriB complexed with a short oligo shows that although PriB is structurally similar to SSB, it binds ssDNA differently [Huang06]. By shift assay, PriB binds both ssDNA and ssRNA equally well [Liu04a].

PriB is required for "constitutive stable DNA replication," that is DNA replication that occurs in the absence of protein synthesis in an rnha mutant [Sandler05].

Though priB nulls have very little phenotypic effect, priBC double nulls demonstrate slow growth and reduced viability [Sandler99]. Certain priB mutants are also deficient in maintenance of some kinds of plasmids [Berges97].

Citations: [Allen91, Zavitz91]

Gene Citations: [Allen91]

Locations: cytosol

Map Position: [4,423,543 -> 4,423,857] (95.34 centisomes)
Length: 315 bp / 104 aa

Molecular Weight of Polypeptide: 11.442 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013742 , CGSC:29153 , DIP:DIP-10563N , EchoBASE:EB0757 , EcoGene:EG10764 , EcoliWiki:b4201 , ModBase:P07013 , OU-Microarray:b4201 , PortEco:priB , PR:PRO_000023592 , Protein Model Portal:P07013 , RefSeq:NP_418622 , RegulonDB:EG10764 , SMR:P07013 , String:511145.b4201 , UniProt:P07013

Relationship Links: InterPro:IN-FAMILY:IPR000424 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR023646 , PDB:Structure:1TXY , PDB:Structure:1V1Q , PDB:Structure:1WOC , PDB:Structure:2CCZ , PDB:Structure:2PNH , Pfam:IN-FAMILY:PF00436 , Prosite:IN-FAMILY:PS50935

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006270 - DNA replication initiation Inferred from experiment [Sandler05]
GO:0006276 - plasmid maintenance Inferred from experiment [Berges97]
GO:0006260 - DNA replication Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0006269 - DNA replication, synthesis of RNA primer Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003697 - single-stranded DNA binding Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Low82]
GO:0005515 - protein binding Inferred from experiment [Lopper07]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0030894 - replisome Inferred by computational analysis [GOA01]
GO:1990077 - primosome complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: information transfer DNA related DNA replication

Essentiality data for priB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Yamamoto09]

Subunit of: primosome

Subunit composition of primosome = [(DnaB)6][(DnaT)3][(PriB)2][PriA][PriC][DnaG]
         replicative DNA helicase = (DnaB)6 (extended summary available)
         primosomal protein DnaT = (DnaT)3 (extended summary available)
                 primosomal protein DnaT = DnaT
         primosomal replication protein N = (PriB)2 (extended summary available)
         primosome factor N' = PriA (extended summary available)
         primosomal replication protein N'' = PriC (extended summary available)
         DNA primase = DnaG (extended summary available)

Summary:
The primosome is a six-protein complex that appears to be involved in restart of stalled replication forks, as well as in replication initiation in certain phages and plasmids. See the individual subunit entries for additional information on the function of the primosome.

The primosome undergoes ordered assembly beginning with PriA binding to DNA. Following this, PriB binds to PriA, then DnaT binds. After this, DnaC loads DnaB in an ATP-dependent manner. DnaG associates with the complex and synthesizes an RNA primer [Ng96]. Despite its absence from this model of ordered assembly, PriC is also found in isolated intact primosomes [Ng96a]. Note that the primosome components have many functions in the cell that do not require the full primosome.


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Allen91, Zavitz91, UniProt11]
UniProt: Removed.
Conserved-Region 2 -> 101
[UniProt09]
UniProt: SSB;
Chain 2 -> 104
[UniProt09]
UniProt: Primosomal replication protein n;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b4201 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10764; confirmed by SwissProt match.


References

Allen91: Allen GC, Kornberg A (1991). "The priB gene encoding the primosomal replication n protein of Escherichia coli." J Biol Chem 1991;266(18);11610-3. PMID: 1646811

Allen93: Allen GC, Kornberg A (1993). "Assembly of the primosome of DNA replication in Escherichia coli." J Biol Chem 268(26);19204-9. PMID: 8366072

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

Berges97: Berges H, Oreglia J, Joseph-Liauzun E, Fayet O (1997). "Isolation and characterization of a priB mutant of Escherichia coli influencing plasmid copy number of delta rop ColE1-type plasmids." J Bacteriol 179(3);956-8. PMID: 9006055

Cadman05: Cadman CJ, Lopper M, Moon PB, Keck JL, McGlynn P (2005). "PriB stimulates PriA helicase via an interaction with single-stranded DNA." J Biol Chem 280(48);39693-700. PMID: 16188886

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, 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."

Heller05: Heller RC, Marians KJ (2005). "The disposition of nascent strands at stalled replication forks dictates the pathway of replisome loading during restart." Mol Cell 17(5);733-43. PMID: 15749022

Huang06: Huang CY, Hsu CH, Sun YJ, Wu HN, Hsiao CD (2006). "Complexed crystal structure of replication restart primosome protein PriB reveals a novel single-stranded DNA-binding mode." Nucleic Acids Res 34(14);3878-86. PMID: 16899446

Liu04a: Liu JH, Chang TW, Huang CY, Chen SU, Wu HN, Chang MC, Hsiao CD (2004). "Crystal structure of PriB, a primosomal DNA replication protein of Escherichia coli." J Biol Chem 279(48);50465-71. PMID: 15383524

Liu96c: Liu J, Nurse P, Marians KJ (1996). "The ordered assembly of the phiX174-type primosome. III. PriB facilitates complex formation between PriA and DnaT." J Biol Chem 271(26);15656-61. PMID: 8663106

Lopper04: Lopper M, Holton JM, Keck JL (2004). "Crystal structure of PriB, a component of the Escherichia coli replication restart primosome." Structure (Camb) 12(11);1967-75. PMID: 15530361

Lopper07: Lopper M, Boonsombat R, Sandler SJ, Keck JL (2007). "A hand-off mechanism for primosome assembly in replication restart." Mol Cell 26(6);781-93. PMID: 17588514

Low82: Low RL, Shlomai J, Kornberg A (1982). "Protein n, a primosomal DNA replication protein of Escherichia coli. Purification and characterization." J Biol Chem 257(11);6242-50. PMID: 6281262

Ng96: Ng JY, Marians KJ (1996). "The ordered assembly of the phiX174-type primosome. I. Isolation and identification of intermediate protein-DNA complexes." J Biol Chem 271(26);15642-8. PMID: 8663104

Ng96a: Ng JY, Marians KJ (1996). "The ordered assembly of the phiX174-type primosome. II. Preservation of primosome composition from assembly through replication." J Biol Chem 271(26);15649-55. PMID: 8663105

Ponomarev03: Ponomarev VA, Makarova KS, Aravind L, Koonin EV (2003). "Gene duplication with displacement and rearrangement: origin of the bacterial replication protein PriB from the single-stranded DNA-binding protein Ssb." J Mol Microbiol Biotechnol 5(4);225-9. PMID: 12867746

Sandler00: Sandler SJ (2000). "Multiple genetic pathways for restarting DNA replication forks in Escherichia coli K-12." Genetics 155(2);487-97. PMID: 10835375

Sandler05: Sandler SJ (2005). "Requirements for replication restart proteins during constitutive stable DNA replication in Escherichia coli K-12." Genetics 169(4);1799-806. PMID: 15716497

Sandler99: Sandler SJ, Marians KJ, Zavitz KH, Coutu J, Parent MA, Clark AJ (1999). "dnaC mutations suppress defects in DNA replication- and recombination-associated functions in priB and priC double mutants in Escherichia coli K-12." Mol Microbiol 34(1);91-101. PMID: 10540288

Shioi05: Shioi S, Ose T, Maenaka K, Shiroishi M, Abe Y, Kohda D, Katayama T, Ueda T (2005). "Crystal structure of a biologically functional form of PriB from Escherichia coli reveals a potential single-stranded DNA-binding site." Biochem Biophys Res Commun 326(4);766-76. PMID: 15607735

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

UniProt11: 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 manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Yamamoto09: Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M, Wanner BL, Mori H (2009). "Update on the Keio collection of Escherichia coli single-gene deletion mutants." Mol Syst Biol 5;335. PMID: 20029369

Zavitz91: Zavitz KH, DiGate RJ, Marians KJ (1991). "The priB and priC replication proteins of Escherichia coli. Genes, DNA sequence, overexpression, and purification." J Biol Chem 266(21);13988-95. PMID: 1856227

Other References Related to Gene Regulation

Maciag11: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

Shimada13b: Shimada T, Yoshida H, Ishihama A (2013). "Involvement of cyclic AMP receptor protein in regulation of the rmf gene encoding the ribosome modulation factor in Escherichia coli." J Bacteriol 195(10);2212-9. PMID: 23475967


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 21, 2014, BIOCYC13B.