A simplified mathematical model of directional DNA site-specific recombination by serine integrases

Pokhilko, A., Zhao, J., Stark, W. M. , Colloms, S. D. and Ebenhöh, O. (2016) A simplified mathematical model of directional DNA site-specific recombination by serine integrases. Journal of the Royal Society: Interface, 14, 20160618. (doi:10.1098/rsif.2016.0618) (PMID:28077763) (PMCID:PMC5310728)

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Abstract

Serine integrases catalyse site-specific recombination to integrate and excise bacteriophage genomes into and out of their host's genome. These enzymes exhibit remarkable directionality; in the presence of the integrase alone, recombination between attP and attB DNA sites is efficient and irreversible, giving attL and attR products which do not recombine further. However, in the presence of the bacteriophage-encoded recombination directionality factor (RDF), integrase efficiently promotes recombination between attL and attR to re-form attP and attB. The DNA substrates and products of both reactions are approximately isoenergetic, and no cofactors (such as adenosine triphosphate) are required for recombination. The thermodynamic driving force for directionality of these reactions is thus enigmatic. Here, we present a minimal mathematical model which can explain the directionality and regulation of both ‘forward’ and ‘reverse’ reactions. In this model, the substrates of the ‘forbidden’ reactions (between attL and attR in the absence of RDF, attP and attB in the presence of RDF) are trapped as inactive protein–DNA complexes, ensuring that these ‘forbidden’ reactions are extremely slow. The model is in good agreement with the observed in vitro kinetics of recombination by ϕC31 integrase, and defines core features of the system necessary and sufficient for directionality.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Stark, Professor William and Colloms, Dr Sean and Zhao, Miss Jia and Pokhilko, Dr Alexandra
Authors: Pokhilko, A., Zhao, J., Stark, W. M., Colloms, S. D., and Ebenhöh, O.
College/School:College of Medical Veterinary and Life Sciences > Institute of Molecular Cell and Systems Biology
Journal Name:Journal of the Royal Society: Interface
Publisher:The Royal Society
ISSN:1742-5689
ISSN (Online):1742-5662
Copyright Holders:Copyright © 2017 The Authors
First Published:First published in Journal of the Royal Society: Interface 14:20160618
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
589142A platform for rapid and precise DNA module rearrangements in Synthetic BiologyWilliam StarkBiotechnology and Biological Sciences Research Council (BBSRC)BB/K003356/1RI MOLECULAR CELL & SYSTEMS BIOLOGY