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

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

Synonyms: srgA, replication factor Y

Regulation Summary Diagram

Regulation summary diagram for priA

Component of: primosome (summary available)

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 [Rangarajan02a]. 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 [Liu99, 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 [Liu99a].

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, Allen93, Jones99]. 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 [Lee90, 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, Lee92].

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 [Liu96, Cadman05]. PriA activity doubles in the completed primosome [Allen93]. 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 [Tanaka02, Chen04a]. Helicase activity is not required for this binding [Tanaka03]. 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, Lee90a, Ouzounis91]

Locations: cytosol

Map Position: [4,122,635 <- 4,124,833] (88.86 centisomes, 320°)
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

Gene-Reaction Schematic

GO Terms:
Biological Process:
Inferred from experimentInferred by computational analysisGO:0006260 - DNA replication [UniProtGOA11a, GOA01a, Rangarajan02a]
Inferred from experimentGO:0006261 - DNA-dependent DNA replication [Liu99]
Inferred from experimentInferred by computational analysisGO:0006268 - DNA unwinding involved in DNA replication [GOA06, Lee87]
Inferred from experimentGO:0006270 - DNA replication initiation [Masai94]
Inferred from experimentGO:0006276 - plasmid maintenance [Lee91]
Inferred from experimentGO:0006302 - double-strand break repair [Kogoma96]
Inferred from experimentGO:0006310 - DNA recombination [Kogoma96]
Inferred from experimentGO:0010332 - response to gamma radiation [Kogoma96]
Inferred from experimentGO:0046677 - response to antibiotic [Kogoma96]
Inferred by computational analysisGO:0006269 - DNA replication, synthesis of RNA primer [UniProtGOA11a]
Inferred by computational analysisGO:0032508 - DNA duplex unwinding [GOA01a]
Molecular Function:
Inferred from experimentInferred by computational analysisGO:0004386 - helicase activity [UniProtGOA11a, Lee87]
Inferred from experimentGO:0005515 - protein binding [Kozlov10, Lopper07]
Inferred from experimentGO:0043140 - ATP-dependent 3'-5' DNA helicase activity [Lee90]
Inferred by computational analysisGO:0000166 - nucleotide binding [UniProtGOA11a]
Inferred by computational analysisGO:0003676 - nucleic acid binding [GOA01a]
Inferred by computational analysisGO:0003677 - DNA binding [UniProtGOA11a, GOA06, GOA01a]
Inferred by computational analysisGO:0004003 - ATP-dependent DNA helicase activity [GOA06, GOA01a]
Inferred by computational analysisGO:0005524 - ATP binding [UniProtGOA11a, GOA06, GOA01a]
Inferred by computational analysisGO:0008270 - zinc ion binding [GOA06]
Inferred by computational analysisGO:0016787 - hydrolase activity [UniProtGOA11a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Cellular Component:
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]
Inferred by computational analysisGO:1990077 - primosome complex [UniProtGOA11a, GOA06]

MultiFun Terms: information transferDNA relatedDNA replication

Essentiality data for priA knockouts:

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

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

Protein sequence of primosome factor N' with features indicated

Feature Class Location Attached Group Citations Comment
Sequence-Conflict 156  
Inferred by curator[Lee90a, UniProt15]
UniProt: (in Ref. 1; AAA24416).
Conserved-Region 211 -> 377  
Inferred by computational analysis[UniProt15]
UniProt: Helicase ATP-binding.
Nucleotide-Phosphate-Binding-Region 224 -> 231 ATP
Inferred by computational analysis[UniProt15]
UniProt: ATP.
Mutagenesis-Variant 226  
Inferred from experiment[Tanaka03]
UniProt: Strong decrease in ATPase and helicase activities. Does not affect DNA binding.
Mutagenesis-Variant 230  
Inferred from experiment[Tanaka03, Jones99]
Inferred from experiment[Tanaka03, Jones99]
K → D: Lack of ATPase activity and strong decrease in helicase activity. Does not affect DNA binding.
K → R: Lack of helicase activity. Decreases Mu DNA replication.
Mutagenesis-Variant 320  
Inferred from experiment[Tanaka03]
UniProt: Strong decrease in ATPase and helicase activities. Decreases DNA binding.
Protein-Segment 320 -> 323  
Author statement[UniProt15]
UniProt: DEAH box; Sequence Annotation Type: short sequence motif.
Zn-Finger-Region 436 -> 448  
Inferred by computational analysis[UniProt15]
UniProt: C4-type.
Conserved-Region 447 -> 638  
Inferred by computational analysis[UniProt15]
UniProt: Helicase C-terminal.
Zn-Finger-Region 463 -> 479  
Inferred by computational analysis[UniProt15]
UniProt: C4-type.
Mutagenesis-Variant 584  
Inferred from experiment[Tanaka03]
UniProt: Does not affect DNA binding, but impairs ATPase activity.
Sequence-Conflict 621  
Inferred by curator[Lee90a, UniProt15]
UniProt: (in Ref. 1; AAA24416).
Sequence-Conflict 649  
Inferred by curator[Nurse90, UniProt15]
UniProt: (in Ref. 2; BAA00491).

Sequence Pfam Features

Protein sequence of primosome factor N' with features indicated

Feature Class Location Citations Comment
Pfam PF00270 203 -> 362
Inferred by computational analysis[Finn14]
DEAD : DEAD/DEAH box helicase
Pfam PF00271 492 -> 589
Inferred by computational analysis[Finn14]
Helicase_C : Helicase conserved C-terminal domain

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram


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


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

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

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

Chen04a: 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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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."

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

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

Jones99: 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

Lee90: 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

Lee90a: 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

Lee92: 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

Liu96: 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

Liu99: 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

Liu99a: 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

Rangarajan02a: 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

Tanaka02: 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

Tanaka03: 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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." 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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