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Modeling DNA Unwinding by AddAB Helicase–Nuclease and Modulation by Chi Sequences: Comparison with AdnAB and RecBCD

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Abstract

Introduction

AddAB enzyme is a helicase–nuclease complex that initiates recombinational repair of double-stranded DNA breaks. It catalyzes processive DNA unwinding and concomitant resection of the unwound strands, which are modulated by the recognition of a recombination hotspot called Chi in the 3′-terminated strand. Despite extensive structural, biochemical and single molecule studies, the detailed molecular mechanism of DNA unwinding by the complex and modulation by Chi sequence remains unclear.

Methods

A model of DNA unwinding by the AddAB complex and modulation by Chi recognition was presented, based on which the dynamics of AddAB complex was studied analytically.

Results

The theoretical results explain well the available experimental data on effect of DNA sequence on velocity, effect of Chi recognition on velocity, static disorder peculiar to the AddAB complex, and dynamics of pausing of wild-type and mutant AddAB complexes occurring at Chi or Chi-like sequence. Predictions were provided. Comparisons of AddAB complex with other helicase–nuclease complexes such as RecBCD and AdnAB were made.

Conclusions

The study has strong implications for the molecular mechanism of DNA unwinding by the AddAB complex. The intriguing issues are addressed of why Chi recognition is an inefficient process, how AddAB complex pauses upon recognizing Chi sequence, how the paused state transits to the translocating state, why the mutant AddAB with a stronger affinity to Chi sequence has a shorter pausing lifetime, why the pausing lifetime is sensitive to the solution temperature, and so on.

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Notes

  1. It is also possible that the force arising from the cleft closing induced by ATP binding cannot overcome the strong binding force of 2A to ssDNA. Thus, it is expected that after ATP binding the cleft is still kept in the open conformation or 2A is moved in a position between that in the open cleft and that in the closed cleft by distorting the ssDNA, both causing appearance of the internal tension. These are consistent with the structural data for AddAB structures bound with DNA containing Chi sequence.10 Then, the release of ATP-hydrolysis products makes 2A in the position in the open cleft with the disappearance of the internal tension. Thus, multiple ATPase cycles take place with no movement of 1A along DNA.

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Acknowledgment

This work was supported by the National Natural Science Foundation of China (Grant No. 11775301).

Conflict of interests

Ping Xie declares that he has no conflicts of interest.

Ethical standards

No human studies were carried out by the author for this article. No animal studies were carried out by the author for this article.

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Authors and Affiliations

  1. Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China

    Ping Xie

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Correspondence to Ping Xie.

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Associate Editor Edward Sander oversaw the review of this article.

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Xie, P. Modeling DNA Unwinding by AddAB Helicase–Nuclease and Modulation by Chi Sequences: Comparison with AdnAB and RecBCD. Cel. Mol. Bioeng. 12, 179–191 (2019). https://doi.org/10.1007/s12195-018-00563-y

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  • DOI: https://doi.org/10.1007/s12195-018-00563-y

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