A simplified mathematical model of directional DNA site-specific recombination by serine integrases
A simplified mathematical model of directional DNA site-specific recombination by serine integrases
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DOI：
10.1098/rsif.2016.0618
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发表时间：
2017-01-01
影响因子：
3.9
通讯作者：
Ebenhoeh, Oliver
中科院分区：
文献类型：
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作者：
Pokhilko, Alexandra;Zhao, Jia;Ebenhoeh, Oliver
丝氨酸整合酶催化位点特异性重组，将噬菌体基因组整合到宿主基因组中或从其宿主基因组中切除。这些酶表现出显着的方向性；仅在整合酶存在的情况下，attP 和 attB DNA 位点之间的重组是有效且不可逆的，产生不会进一步重组的 attL 和 attR 产物。然而，在噬菌体编码的重组方向性因子 (RDF) 存在的情况下，整合酶有效地促进 attL 和 attR 之间的重组，从而重新形成 attP 和 attB。两个反应的 DNA 底物和产物大致等能量，重组不需要辅因子（如三磷酸腺苷）。因此，这些反应方向性的热力学驱动力是神秘的。在这里，我们提出了一个最小的数学模型，可以解释“正向”和“反向”反应的方向性和调节。在此模型中，“禁止”反应的底物（在不存在 RDF 的情况下，attL 和 attR 之间，在存在 RDF 的情况下，attP 和 attB 之间）被捕获为无活性的蛋白质-DNA 复合物，确保这些“禁止”反应极其缓慢。该模型与所观察到的 phi C31 整合酶重组的体外动力学非常一致，并定义了系统的方向性必要且充分的核心特征。
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 phi C31 integrase, and defines core features of the system necessary and sufficient for directionality.