Bacterial Primosome

Taku Tanaka, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
Hisao Masai, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan

Published online: April 2010

DOI: 10.1002/9780470015902.a0001048.pub2

Abstract

DNA (deoxyribonucleic acid) replication requires operation of a molecular machinery which efficiently synthesises of nucleotide chains on both strands. This process requires not only the enzymes synthesising DNA (DNA polymerases) but also those providing primer RNAs (ribonucleic acid) and continuously melting the duplex DNA. The primosome refers to a protein complex capable of processive unwinding of duplex DNA and primer RNA synthesis on the lagging strand at a replication fork. The prepriming proteins, DNA helicase and primase are sequentially assembled on the template DNA to generate primosome. Once assembled, it, in conjunction with DNA polymerases, facilitates DNA chain elongation. The assembly of bacterial primosome is triggered by an ‘initiator’ protein including DnaA and PriA, which recognise the site of assembly. Primosome is reassembled in replication restart process at stalled or processed replication forks, triggered by PriA. Thus, primosome constitutes an essential component for active replication fork machinery.

Key concepts:

  • Replication fork is the site of DNA replication where two replicating single‐stranded DNA separates.

  • Primer RNA is a short stretch of RNA, the 3′‐terminus of which is utilised by DNA polymerases for DNA elongation.

  • Primosome is a name given to the protein complex capable of duplex DNA unwinding and primer RNA synthesis at the replication fork.

  • oriC is the replication origin of chromosome. The initiation site of bacterial chromosomal DNA replication under a normal growth condition.

  • DnaA is the initiator protein for bacterial chromosomal replication, which binds to oriC to assemble a primosome.

  • PriA is a conserved replication factor which triggers assembly of the so‐called ϕX174‐type primosome, which is assembled at a stalled replication fork for replication restart.

  • Stalled replication fork, the replication fork the movement of which is blocked by internal and external ‘replication stress’ including DNA damages and depletion of nucleotide precursors.

  • Replication restart is a process of reassembly of primosome at a stalled replication fork to resume DNA chain elongation.

  • Recombination intermediate is the intermediate structure (e.g. D‐loop structure) of homologous recombination reaction.

  • DNA helicase is a protein capable of unwinding a duplex DNA at a replication fork by using the energy derived from the hydrolysis of nucleotides.

  • Prepriming proteins are proteins required for the stage preceding the association of the primase (an enzyme synthesising primer RNAs) during the assembly of a primosome.

Keywords: DnaA; PriA; DnaB helicase; DnaG primase; replication fork

Figure 1.

Two representative modes of primosome assembly for DNA replication in E. coli. PriA‐dependent primosome is assembled at a small single‐stranded hairpin structure, whereas DnaA‐dependent primosome is assembled at oriCDNA as well as at a hairpin containing dnaA box (A site). The two modes differ in the requirement of proteins involved in the prepriming stage. Hypothetical structures for the preprimosomes are shown and the association of DnaG primase with them results in functional primosomes. The PriA‐dependent ‘ϕX174‐type’ primosome can be assembled at a recombination intermediate or at a stalled replication fork.

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References

Arai K, Low R and Kornberg A (1981) Movement and site selection for priming by the primosome in phage ϕX174 DNA replication. Proceedings of the National Academy of Sciences of the USA 78: 707–711.

Bruand C, Velten M, McGovern S et al. (2005) Functional interplay between the Bacillus subtilis DnaD and DnaB proteins essential for initiation and re‐initiation of DNA replication. Molecular Microbiology 55: 1138–1150.

Chen HW, North SH and Nakai H (2004) Properties of the PriA helicase domain and its role in binding PriA to specific DNA structures. Journal of Biological Chemistry 279: 38503–38512.

Heller RC and Marians KJ (2005) Unwinding of the nascent lagging strand by Rep and PriA enables the direct restart of stalled replication forks. Journal of Biological Chemistry 280: 34143–34151.

Jones JM and Nakai H (1999) Duplex opening by primosome protein PriA for replisome assembly on a recombination intermediate. Journal of Molecular Biology 289: 503–515.

Kogoma T, Cadwell GX, Barnard KG and Asai T (1996) Requirement of the DNA replication priming protein, PriA, for homologous recombination and double‐strand break repair. Journal of Bacteriology 178: 1258–1264.

Kornberg A and Baker TA (1992) DNA Replication, 2nd edn. New York: Freeman.

Liu J and Marians KJ (1999) PriA‐directed assembly of a primosome on D‐loop DNA. Journal of Biological Chemistry 274: 25033–25041.

Lopper M, Holten JM and Kech JL (2004) Crystal structure of PriB, a component of the E. coli replication restart primosome. Structure 12: 1967–1975.

Masai H, Asai T, Kubota Y, Arai k and Kogoma T (1994) Escherichia Coli PriA protein is essential for inducible and constitutive stable DNA replication. EMBO Journal 13: 5338–5345.

Masai H, Nomura N and Arai K (1990) The ABC primosome: a novel priming system employing dnaA, dnaB, dnaC, and primase on a hairpin containing a dnaA box sequence. Journal of Biological Chemistry 265: 15124–15144.

McGlynn P, Al‐Deib AA, Liu J, Marians KJ and Lloyd RG (1997) The DNA replication protein PriA and the recombination protein RecG bind D‐loops. Journal of Molecular Biology 270: 212–221.

Mizukoshi T, Tanaka T, Arai K, Kohda D and Masai H (2003) A critical role of the 3′ terminus of nascent DNA chains in recognition of stalled replication forks. Journal of Biological Chemistry 278: 42234–42239.

Ng JY and Marians KJ (1996) The ordered assembly of the ϕX174‐type primosome. Journal of Biological Chemistry 271: 15642–15648.

Nossal NG (1992) Protein‐protein interactions at a DNA replication fork: bacteriophage T4 as a model. FASEB Journal 6: 871–878.

Sandler SJ and Marians KJ (2000) Role of PriA in replication fork reactivation in E. coli. Journal of Bacteriology 182: 9–13.

Sasaki K, Ose T, Okamoto N et al. (2007) Structural basis of the 3′‐end recognition of a leading strand in stalled replication forks by PriA. EMBO Journal 26: 2584–2593.

Shlomai J and Kornberg A (1980) An E. coli replication protein that recognizes a unique sequence within a hairpin region in ϕX174 DNA. Proceedings of the National Academy of Sciences of the USA 77: 799–803.

Tanaka T, Mizukoshi T, Taniyama C et al. (2002) DNA binding of PriA protein requires cooperation of the N‐ternimal D‐loop/arrested‐fork binding and C‐terminal helicase domains. Journal of Biological Chemistry 277: 38062–38071.

Further Reading

Marians KJ (1992) Prokaryotic DNA replication. Annual Review of Biochemistry 61: 673–719.

Related Sub-Topics:

Nucleic Acids: Structure, Function, Metabolism | Replication and Recombination | Enzymes: Structure and Action Mechanism | DNA Structure and Function | DNA Damage and Repair | Transcription of DNA
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Article Title: Bacterial Primosome
 
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Tanaka, Taku, and Masai, Hisao(Apr 2010) Bacterial Primosome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001048.pub2]