Synthesis of lagging strand, how does the lagging strand polymerase recycle?

Based on the polarity of double stranded DNA molecule and characteristic of DNA polymerase III Holoenzyme that can only synthesize DNA in 5′-3′ direction, replication is carried in a discontinuous manner. There are two core polymerase on the replisome and each core takes part in leading or lagging synthesis. On the leading template, the new strand is synthesized continuously in the same direction with the fork progression, while on lagging template, the synthesis occurs in the opposite direction with fork movement. Therefore, the synthesis of lagging strand is discontinuous, requires many RNA primers and the recycling of lagging strand polymerase, resulting a number of Okazaki fragment (each Okazaki fragment requires one RNA primer).  Basically, the molecular basis of DNA replication have been widely studied. However, the mechanisms of lagging strand synthesis is not clear yet and still controversial. For example, what is the trigger of lagging strand polymerase recycling, or how the next Okazaki fragment is synthesized?

Various mechanisms have been proposed to explain the recycling of the lagging strand polymerase. Among them, two following models are mostly supported so far.

In the first model, named as “collision release” model, when the lagging polymerase collides the end of the previous Okazaki fragment, it will trigger dissociation of the polymerase from the clamp, leaving the clamp alone on DNA. After that, this free polymerase will bind to a new clamp, assembled on a new RNA primer by the clamp loader, to start synthesis of the next Okazaki fragment. In this model, there will be no gap between two Okazaki fragments.

In the second model (named as “signaling release” or “premature release” model), it is believed that lagging polymerase releases from the clamp before the Okazaki fragment is finished. Therefore, the collision of the replicating lagging strand polymerase with the 5′ end of the previous Okazaki fragment is not required. The signal for this releasing is by new clamp loader or new primer synthesis. As mentioned, synthesis of lagging strand is discontinuous and require many primers. During Okazaki fragments synthesis, primase synthesizes a RNA primer. After that, the clamp is recruited from the solution and loaded onto the newly synthesized primer by the clamp loader (gamma complex in E. coli cell). The loading of the clamp is the trigger for dissociation of the lagging polymerase. After dissociation, this free-polymerase will be assemble to the new clamp to start the next Okazaki fragment synthesis. In this model, there is a possibility of ssDNA gaps between Okazaki fragments.
Figure A. Two major models explaining the recycling of lagging strand polymerase (Nina Y Yao and Mike O’Donnell, 2009). Top: Collision release model, in which the collision of  lagging strand polymerase with the 5′ end of the previous Okazaki fragment is the trigger for dissociation of polymerase. Bottom: Premature release model (or signaling release model), in this model, the collision doesn’t require for lagging strand polymerase recycling. The signal comes from new RNA primer synthesis and new clamp loader.




Jingsong Yang et al. The Control Mechanism for Lagging Strand Polymerase Recycling during Bacteriophage T4 DNA Replication. Molecular Cell, 2006.

Nina Y Yao and Mike O’Donnell. Replisome structure and conformational dynamics underlie fork progression past obstacles. Curr Opin Cell Biol, 2009.

Michael E. O’DonnellS and Arthur Kornberg. Dynamics of DNA Polymerase III Holoenzyme of Escherichia coli in Replication of a Multiprimed Template. The journal of biological chemistry, 1985.

Michael E. O’Donnel. Accessory Proteins Bind a Primed Template and Mediate Rapid Cycling of DNA Polymerase III Holoenzyme from Escherichia coli. The journal of biological chemistry, 1987.
Jong-Bong Lee et al. DNA primase acts as a molecular brake in DNA replication. Nature letters, 2006.



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