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Escherichia coli K-12 substr. MG1655 Polypeptide: primosome factor N'



Gene: priA Accession Numbers: EG10763 (EcoCyc), b3935, ECK3927

Synonyms: srgA, replication factor Y

Regulation Summary Diagram: ?

Component of: primosome (summary available)

Summary:
The role of PriA in the cell appears to be the restart of stalled replication forks. PriA, along with DNA polymerase II, is required to restart DNA synthesis immediately following UV exposure [Rangarajan02]. Based on genetic interactions, there seem to be two replication restart pathways that require PriA, one using RecG, the other using RuvABC [Meddows04, Gregg02].

PriA binds to the 3' terminus of nascent DNA at stalled replication forks in vitro, leading to assembly of the full primosome at the binding site [Mizukoshi03]. PriA preferentially binds to stalled forks with D loops, which are intermediates in recombination-based recovery from a stall [Liu99f, McGlynn97]. Larger single-stranded gaps at the stall site favor PriC-mediated restart rather than PriA involvement [Heller05]. PriA binding is most effective when the lagging strand is duplex and the leading strand is single stranded [Jones01]. D loop binding leads to assembly of the full primosome at the stall site [Liu99g].

In many plasmids and phages, PriA and the primosome function in initiation of normal DNA replication. In this context, PriA binds to the primosome assembly site (PAS), a double-hairpin DNA structure that acts as the origin of replication for replicative DNA synthesis [Greenbaum85, Soeller82, Zipursky81, Zipursky80, Allen93a, Jones99b]. Following PAS binding, PriA translocates 3' to 5' along ssDNA in an ATP-dependent fashion, after which it can move onto and unwind duplex DNA, a process that also uses ATP [Lee90a, Lee87]. This PriA-mediated unwinding moves just as fast as unwinding catalyzed by the normal replicative helicase, DnaB, and is stimulated by interaction with single-strand binding protein (SSB) via the SSB carboxy-terminus [Mok87, Cadman04]. PriA helicase activity is blocked by Tus bound at ter replication termination sites [Hiasa92, Lee92b].

PriA binding is the first step in assembly of the primosome, a multiprotein complex that restarts stalled replication forks in E. coli and initiates replication in various plasmids and phages [Ng96]. The primosomal protein PriB helps PriA bind DnaT, as well as stimulating the processivity and helicase activity of PriA [Liu96d, Cadman05]. PriA activity doubles in the completed primosome [Allen93a]. Notably, PriA that lacks its helicase and translocation activities can still catalyze primosome assembly, and this alone appears to be sufficient to correct defects in homologous recombination and double-strand-break repair that are normally present in priA null mutants [Zavitz92, Kogoma96].

PriA binds ssDNA as a monomer via a single DNA-binding site, binding to as few as 8 nucleotides [Jezewska00, Jezewska00a]. This binding occurs in the PriA amino-terminal domain, though the helicase domain works together with it synergistically to allow high-affinity binding of D loops at replication forks [Tanaka02a, Chen04d]. Helicase activity is not required for this binding [Tanaka03b]. The kinetics of PriA binding to ssDNA have been examined in detail [Galletto04].

The amino-terminal domain of PriA has been crystallized [Sasaki06].

PriA is required for inducible and constitutive stable DNA replication in the absence of protein synthesis [Masai94].

priA null mutants are unable to generate phiX174 phage or maintain plasmids that use an E. coli origin of replication. They also have growth defects and a filamentous phenotype [Lee91]. The SOS response is induced in these mutants [Nurse91]. Loss of PriA helicase activity suppresses the deleterious effects of the loss of RecG recombinational helicase function [AlDeib96].

Citations: [Wickner75, Lee90b, Ouzounis91]

Locations: cytosol

Map Position: [4,122,635 <- 4,124,833] (88.86 centisomes)
Length: 2199 bp / 732 aa

Molecular Weight of Polypeptide: 81.655 kD (from nucleotide sequence), 78 kD (experimental) [Nurse90 ]

Unification Links: ASAP:ABE-0012860 , CGSC:27611 , DIP:DIP-10562N , EchoBASE:EB0756 , EcoGene:EG10763 , EcoliWiki:b3935 , Mint:MINT-1274231 , ModBase:P17888 , OU-Microarray:b3935 , PortEco:priA , PR:PRO_000023591 , Protein Model Portal:P17888 , RefSeq:NP_418370 , RegulonDB:EG10763 , SMR:P17888 , String:511145.b3935 , UniProt:P17888

Relationship Links: InterPro:IN-FAMILY:IPR001650 , InterPro:IN-FAMILY:IPR005259 , InterPro:IN-FAMILY:IPR011545 , InterPro:IN-FAMILY:IPR014001 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:2D7E , PDB:Structure:2D7G , PDB:Structure:2D7H , PDB:Structure:2DWL , PDB:Structure:2DWM , PDB:Structure:2DWN , Pfam:IN-FAMILY:PF00270 , Pfam:IN-FAMILY:PF00271 , Prosite:IN-FAMILY:PS51192 , Prosite:IN-FAMILY:PS51194 , Smart:IN-FAMILY:SM00487 , Smart:IN-FAMILY:SM00490

In Paralogous Gene Group: 563 (2 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006260 - DNA replication Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Rangarajan02]
GO:0006261 - DNA-dependent DNA replication Inferred from experiment [Liu99f]
GO:0006268 - DNA unwinding involved in DNA replication Inferred from experiment [Lee87]
GO:0006270 - DNA replication initiation Inferred from experiment [Masai94]
GO:0006276 - plasmid maintenance Inferred from experiment [Lee91]
GO:0006302 - double-strand break repair Inferred from experiment [Kogoma96]
GO:0006310 - DNA recombination Inferred from experiment [Kogoma96]
GO:0010332 - response to gamma radiation Inferred from experiment [Kogoma96]
GO:0046677 - response to antibiotic Inferred from experiment [Kogoma96]
GO:0006269 - DNA replication, synthesis of RNA primer Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0004386 - helicase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Lee87]
GO:0005515 - protein binding Inferred from experiment [Kozlov10, Lopper07]
GO:0043140 - ATP-dependent 3'-5' DNA helicase activity Inferred from experiment [Lee90a]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:1990077 - primosome complex Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: information transfer DNA related DNA replication

Essentiality data for priA knockouts: ?

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

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
Sequence-Conflict 156
[Nurse90, Lee90b, UniProt10]
Alternate sequence: A → R; UniProt: (in Ref. 1 and 2);
Conserved-Region 211 -> 377
[UniProt09]
UniProt: Helicase ATP-binding;
Nucleotide-Phosphate-Binding-Region 224 -> 231
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Protein-Segment 320 -> 323
[UniProt10]
UniProt: DEEH box; Sequence Annotation Type: short sequence motif;
Zn-Finger-Region 436 -> 448
[UniProt10a]
UniProt: C4-type; Non-Experimental Qualifier: potential;
Conserved-Region 447 -> 638
[UniProt09]
UniProt: Helicase C-terminal;
Zn-Finger-Region 463 -> 479
[UniProt10a]
UniProt: C4-type; Non-Experimental Qualifier: potential;
Sequence-Conflict 621
[Nurse90, Lee90b, UniProt10]
Alternate sequence: A → R; UniProt: (in Ref. 1 and 2);
Sequence-Conflict 649
[Nurse90, UniProt10]
Alternate sequence: A → V; UniProt: (in Ref. 2; BAA00491);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3935 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10763; confirmed by SwissProt match.


References

AlDeib96: Al-Deib AA, Mahdi AA, Lloyd RG (1996). "Modulation of recombination and DNA repair by the RecG and PriA helicases of Escherichia coli K-12." J Bacteriol 178(23);6782-9. PMID: 8955297

Allen93a: 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

Cadman04: Cadman CJ, McGlynn P (2004). "PriA helicase and SSB interact physically and functionally." Nucleic Acids Res 32(21);6378-87. PMID: 15576682

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

Chen04d: Chen HW, North SH, Nakai H (2004). "Properties of the PriA helicase domain and its role in binding PriA to specific DNA structures." J Biol Chem 279(37);38503-12. PMID: 15252043

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

Galletto04: Galletto R, Jezewska MJ, Bujalowski W (2004). "Multistep sequential mechanism of Escherichia coli helicase PriA protein-ssDNA interactions. Kinetics and energetics of the active ssDNA-searching site of the enzyme." Biochemistry 43(34);11002-16. PMID: 15323559

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

Greenbaum85: Greenbaum JH, Marians KJ (1985). "Mutational analysis of primosome assembly sites. Evidence for alternative DNA structures." J Biol Chem 260(22);12266-72. PMID: 2931433

Gregg02: Gregg AV, McGlynn P, Jaktaji RP, Lloyd RG (2002). "Direct rescue of stalled DNA replication forks via the combined action of PriA and RecG helicase activities." Mol Cell 9(2);241-51. PMID: 11864599

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

Hiasa92: Hiasa H, Marians KJ (1992). "Differential inhibition of the DNA translocation and DNA unwinding activities of DNA helicases by the Escherichia coli Tus protein." J Biol Chem 267(16);11379-85. PMID: 1317865

Jezewska00: Jezewska MJ, Bujalowski W (2000). "Interactions of Escherichia coli replicative helicase PriA protein with single-stranded DNA." Biochemistry 39(34);10454-67. PMID: 10956036

Jezewska00a: Jezewska MJ, Rajendran S, Bujalowski W (2000). "Escherichia coli replicative helicase PriA protein-single-stranded DNA complex. Stoichiometries, free energy of binding, and cooperativities." J Biol Chem 275(36);27865-73. PMID: 10875934

Jones01: Jones JM, Nakai H (2001). "Escherichia coli PriA helicase: fork binding orients the helicase to unwind the lagging strand side of arrested replication forks." J Mol Biol 312(5);935-47. PMID: 11580240

Jones99b: Jones JM, Nakai H (1999). "Duplex opening by primosome protein PriA for replisome assembly on a recombination intermediate." J Mol Biol 289(3);503-16. PMID: 10356325

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

Kogoma96: Kogoma T, Cadwell GW, Barnard KG, Asai T (1996). "The DNA replication priming protein, PriA, is required for homologous recombination and double-strand break repair." J Bacteriol 178(5);1258-64. PMID: 8631700

Kozlov10: Kozlov AG, Jezewska MJ, Bujalowski W, Lohman TM (2010). "Binding specificity of Escherichia coli single-stranded DNA binding protein for the chi subunit of DNA pol III holoenzyme and PriA helicase." Biochemistry 49(17);3555-66. PMID: 20329707

Lee87: Lee MS, Marians KJ (1987). "Escherichia coli replication factor Y, a component of the primosome, can act as a DNA helicase." Proc Natl Acad Sci U S A 84(23);8345-9. PMID: 2825188

Lee90a: Lee MS, Marians KJ (1990). "Differential ATP requirements distinguish the DNA translocation and DNA unwinding activities of the Escherichia coli PRI A protein." J Biol Chem 265(28);17078-83. PMID: 2170365

Lee90b: Lee EH, Masai H, Allen GC, Kornberg A (1990). "The priA gene encoding the primosomal replicative n' protein of Escherichia coli." Proc Natl Acad Sci U S A 1990;87(12);4620-4. PMID: 2162050

Lee91: Lee EH, Kornberg A (1991). "Replication deficiencies in priA mutants of Escherichia coli lacking the primosomal replication n' protein." Proc Natl Acad Sci U S A 88(8);3029-32. PMID: 1826559

Lee92b: Lee EH, Kornberg A (1992). "Features of replication fork blockage by the Escherichia coli terminus-binding protein." J Biol Chem 267(13);8778-84. PMID: 1533620

Liu96d: 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

Liu99f: Liu J, Xu L, Sandler SJ, Marians KJ (1999). "Replication fork assembly at recombination intermediates is required for bacterial growth." Proc Natl Acad Sci U S A 96(7);3552-5. PMID: 10097074

Liu99g: Liu J, Marians KJ (1999). "PriA-directed assembly of a primosome on D loop DNA." J Biol Chem 274(35);25033-41. PMID: 10455182

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

Masai94: Masai H, Asai T, Kubota Y, Arai K, Kogoma T (1994). "Escherichia coli PriA protein is essential for inducible and constitutive stable DNA replication." EMBO J 13(22);5338-45. PMID: 7525276

McGlynn97: McGlynn P, Al-Deib AA, Liu J, Marians KJ, Lloyd RG (1997). "The DNA replication protein PriA and the recombination protein RecG bind D-loops." J Mol Biol 270(2);212-21. PMID: 9236123

Meddows04: Meddows TR, Savory AP, Lloyd RG (2004). "RecG helicase promotes DNA double-strand break repair." Mol Microbiol 52(1);119-32. PMID: 15049815

Mizukoshi03: Mizukoshi T, Tanaka T, Arai K, Kohda D, Masai H (2003). "A critical role of the 3' terminus of nascent DNA chains in recognition of stalled replication forks." J Biol Chem 278(43);42234-9. PMID: 12917421

Mok87: Mok M, Marians KJ (1987). "The Escherichia coli preprimosome and DNA B helicase can form replication forks that move at the same rate." J Biol Chem 262(34);16644-54. PMID: 2824502

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

Nurse90: Nurse P, DiGate RJ, Zavitz KH, Marians KJ (1990). "Molecular cloning and DNA sequence analysis of Escherichia coli priA, the gene encoding the primosomal protein replication factor Y." Proc Natl Acad Sci U S A 87(12);4615-9. PMID: 2162049

Nurse91: Nurse P, Zavitz KH, Marians KJ (1991). "Inactivation of the Escherichia coli priA DNA replication protein induces the SOS response." J Bacteriol 173(21);6686-93. PMID: 1938875

Ouzounis91: Ouzounis CA, Blencowe BJ (1991). "Bacterial DNA replication initiation factor priA is related to proteins belonging to the 'DEAD-box' family." Nucleic Acids Res 19(24);6953. PMID: 1662369

Rangarajan02: Rangarajan S, Woodgate R, Goodman MF (2002). "Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins." Mol Microbiol 43(3);617-28. PMID: 11929519

Sasaki06: Sasaki K, Ose T, Tanaka T, Mizukoshi T, Ishigaki T, Maenaka K, Masai H, Kohda D (2006). "Crystallization and preliminary crystallographic analysis of the N-terminal domain of PriA from Escherichia coli." Biochim Biophys Acta 1764(1);157-60. PMID: 16226927

Soeller82: Soeller WC, Marians KJ (1982). "Deletion mutants defining the Escherichia coli replication factor Y effector site sequences in pBR322 DNA." Proc Natl Acad Sci U S A 79(23);7253-7. PMID: 6130524

Tanaka02a: Tanaka T, Mizukoshi T, Taniyama C, Kohda D, Arai K, Masai H (2002). "DNA binding of PriA protein requires cooperation of the N-terminal D-loop/arrested-fork binding and C-terminal helicase domains." J Biol Chem 277(41);38062-71. PMID: 12151393

Tanaka03b: Tanaka T, Taniyama C, Arai K, Masai H (2003). "ATPase/helicase motif mutants of Escherichia coli PriA protein essential for recombination-dependent DNA replication." Genes Cells 8(3);251-61. PMID: 12622722

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

Wickner75: Wickner S, Hurwitz J (1975). "Association of phiX174 DNA-dependent ATPase activity with an Escherichia coli protein, replication factor Y, required for in vitro synthesis of phiX174 DNA." Proc Natl Acad Sci U S A 72(9);3342-6. PMID: 127175

Zavitz92: Zavitz KH, Marians KJ (1992). "ATPase-deficient mutants of the Escherichia coli DNA replication protein PriA are capable of catalyzing the assembly of active primosomes." J Biol Chem 267(10);6933-40. PMID: 1313026

Zipursky80: Zipursky SL, Marians KJ (1980). "Identification of two Escherichia coli factor Y effector sites near the origins of replication of the plasmids (ColE1 and pBR322." Proc Natl Acad Sci U S A 77(11);6521-5. PMID: 6109282

Zipursky81: Zipursky SL, Marians KJ (1981). "Escherichia coli factor Y sites of plasmid pBR322 can function as origins of DNA replication." Proc Natl Acad Sci U S A 78(10);6111-5. PMID: 6273849


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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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