The Apl protein of bacteriophage 186 functions both as an excisionase and as a transcriptional regulator; binding to the phage attachment site (att), and also between the major early phage promoters (pR-pL). Like other recombination directionality factors (RDFs), Apl binding sites are direct repeats spaced one DNA helix turn apart. Here, we use in vitro binding studies with purified Apl and pR-pL DNA to show that Apl binds to multiple sites with high cooperativity, bends the DNA and spreads from specific binding sites into adjacent non-specific DNA; features that are shared with other RDFs. By analysing Apl's repression of pR and pL, and the effect of operator mutants in vivo with a simple mathematical model, we were able to extract estimates of binding energies for single specific and non-specific sites and for Apl cooperativity, revealing that Apl monomers bind to DNA with low sequence specificity but with strong cooperativity between immediate neighbours. This model fit was then independently validated with in vitro data. The model we employed here is a simple but powerful tool that enabled better understanding of the balance between binding affinity and cooperativity required for RDF function. A modelling approach such as this is broadly applicable to other systems.

中文翻译：

---

Apl蛋白，双重目的的重组方向因子和噬菌体186的溶菌原性调节剂的定量结合模型。

噬菌体186的Apl蛋白既起切除酶的作用，又起转录调节剂的作用。与噬菌体附着位点（att）以及主要的早期噬菌体启动子（pR-pL）之间的结合。像其他重组方向性因子（RDF）一样，Apl结合位点是直接重复序列，彼此间隔一个DNA螺旋。在这里，我们使用纯化的Apl和pR-pL DNA进行体外结合研究，显示Apl以高协同性结合到多个位点，弯曲DNA并从特异性结合位点扩散到相邻的非特异性DNA中。与其他RDF共享的功能。通过分析Apl对pR和pL的抑制以及体内操纵基因突变体的作用通过简单的数学模型，我们能够提取单个特异性和非特异性位点以及Apl协同作用的结合能的估计值，从而揭示了Apl单体以较低的序列特异性结合DNA，但邻国之间具有很强的协同作用。然后使用体外数据独立验证该模型拟合。我们在这里使用的模型是一个简单但功能强大的工具，可以更好地理解RDF功能所需的绑定亲和力和协作能力之间的平衡。诸如此类的建模方法广泛适用于其他系统。