Bacterial Replication Fork: Synthesis of Lagging Strand


How can an antiparallel DNA (deoxyribonucleic acid) strand be duplicated by a DNA polymerase that synthesises DNA in only one direction? This paradox of DNA synthesis on the lagging strand was dissolved by discovery of Okazaki fragments. The major components of the bacterial replication fork include replicative helicase, primase and DNA polymerase. The loading of replicative helicase, DnaB, is the most critical step for assembly of a primosome, a protein complex responsible for duplex unwinding and primer RNA (ribonucleic acid) synthesis at the replication fork. DNA polymerase may be an asymmetric dimer, each of which may concurrently synthesise leading or lagging strand. Several different modes of primosome assembly have been identified in bacteria. At oriC (origin of chromosome), DnaA‐dependent primosome is assembled for initiation of a round of DNA replication, whereas PriA‐dependent primosome is assembled at stalled replication forks to facilitate replication restart.

Key Concepts:

  • Initiation of DNA replication: DNA replication is initiated by the initiator protein, which specifically recognises and binds to the origin sequence and recruits other primosome components including a DNA helicase.

  • Leading and lagging strands: Leading strand is the one in which the direction of DNA chain elongation and overall fork movement is the same and lagging strand is the one in which they are opposite.

  • Replicative helicase: An enzyme which catalyses continuous unwinding of the parental duplex DNA at the replication fork.

  • Replication fork: The site of DNA replication where two replicating single‐stranded DNA separates.

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

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

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

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

Keywords: replication fork; Okazaki fragment; DNA polymerases; primer RNA; replication restart

Figure 1.

The end/polarity problem of a replication fork and Okazaki fragment model. (a) Unidirectional elongation of DNA chains in only 5′ to 3′ direction by DNA polymerases inevitably generates an unreplicated segment on one strand of template DNA at the replication fork (shown by dotted lines), as a replication fork propagates. (b) Reiji Okazaki proposed that the lagging strand (upper strand in this figure) is synthesised discontinuously through joining of small pieces of nascent DNA (Okazaki fragments). Red arrowed lines and orange wavy lines represent nascent DNA chains and primer RNAs, respectively.

Figure 2.

A model for the bacterial replication fork structure. The model shows concurrent replication of both strands by asymmetric twin DNA polymerases with a looped lagging strand DNA template. DnaB, located on the lagging strand template, unwinds duplex DNA and primase, in association with DnaB, generates primer RNAs for synthesis of multiple Okazaki fragments. SSB () protects the exposed single‐stranded DNA and facilitates the action of DNA polymerase. Swiverase (DNA topoisomerase) eliminates the positive supercoiling which would accumulate in the unreplicated duplex segment, as the replication fork progresses.



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.

Bambara RA, Murante RS and Henricksen LA (1997) Enzymes and reactions at the eukaryotic DNA replication fork. Journal of Biological Chemistry 272: 4647–4650.

Bouche JP, Rowen L and Kornberg A (1978) The RNA primer synthesised by primase to initiate phage G4 DNA replication. Journal of Biological Chemistry 253: 765–679.

Dahlberg JE, Sawyer RC, Taylor JM et al. (1974) Transcription of DNA from the 70S RNA of Rous sarcoma virus. I. Identification of a specific 4S RNA which serves as primer. Journal of Virology 13: 1126–1133.

Geider K and Kornberg A (1974) Conversion of the M13 viral single‐strand to the double‐stranded replicative forms by purified proteins. Journal of Biological Chemistry 249: 3999–4005.

Heller RC and Marians KJ (2006a) Replisome assembly and the direct restart of stalled replication forks. Nature Reviews. Molecular Cell Biology 7: 932–943.

Heller RC and Marians KJ (2006b) Replication fork reactivation downstream of a blocked nascent leading strand. Nature 439: 557–562.

Katou Y, Kanoh Y, Bando M et al. (2003) S‐phase checkpoint proteins Tof1 and Mrc1 form a stable replication‐pausing complex. Nature 424: 1078–1083.

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

Maki H, Maki S and Kornberg A (1988) DNA polymerase III holoenzyme of E. coli. IV. The holoenzyme is an asymmetric dimer with twin active sites. Journal of Biological Chemistry 263: 6570–6578.

Masai H and Arai K (1996) Mechanisms of primer RNA synthesis and D‐loop/R‐loop‐dependent DNA replication in E. coli. Biochimie 78: 1109–1117.

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.

Noguchi E, Noguchi C, McDonald WH, Yates JR and Russell P (2004) Swi1 and Swi3 are components of a replication fork protection complex in fission yeast. Molecular and Cellular Biology 24: 8342–8355.

Okazaki R, Okazaki T, Sakabe K, Sugimoto K and Sugino A (1968) Mechanism of DNA chain growth, I. Possible discontinuity and unusual secondary structure of newly synthesized chains. Proceedings of the National Academy of Sciences of the USA 59: 598–605.

Pages V and Fuchs RP (2003) Uncoupling of leading‐ and lagging‐strand DNA replication during lesion bypass in vivo. Science 23: 1300–1303.

Pursell ZF, Isoz I, Lundstrom E‐B, Johansson E and Kunkel TA (2007) Yeast DNA polymerase ɛ participates in leading‐strand DNA replication. Science 317: 127–130.

Sinha NK, Morris CF and Alberts BM (1980) Efficient in vitro replication of double‐stranded DNA templates by purified T4 bacteriophage replication system. Journal of Biological Chemistry 255: 4290–4303.

Sugino A, Hirose S and Okazaki R (1972) RNA‐linked nascent DNA fragments in E. coli. Proceedings of the National Academy of Sciences of the USA 69: 1863–1867.

Tsurimoto T and Stillman B (1991) Replication factors required for SV40 DNA replication in vitro. II. Switching of DNA polymerase a and d during initiation of leading and lagging strand synthesis. Journal of Biological Chemistry 266: 1961–1968.

Further Reading

Harrington JJ and Lieber MR (1994) The characterization of a mammalian DNA structure‐specific endonuclease. EMBO Journal 13: 1235–1246.

Kornberg A (1989) For the Love of Enzymes. The Odyssey of a Biochemist. Cambridge: Harvard University Press.

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

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Tanaka, Taku, and Masai, Hisao(Apr 2010) Bacterial Replication Fork: Synthesis of Lagging Strand. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0001049.pub2]