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Type: Journal article
Title: A quantitative binding model for the Apl protein, the dual purpose recombination-directionality factor and lysis-lysogeny regulator of bacteriophage 186
Author: Cutts, E.E.
Egan, J.
Dodd, I.B.
Shearwin, K.E.
Citation: Nucleic Acids Research, 2020; 48(16):8914-8926
Publisher: Oxford University Press
Issue Date: 2020
ISSN: 0305-1048
Statement of
Erin E Cutts, J Barry Egan, Ian B Dodd, Keith E Shearwin
Abstract: 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.
Keywords: Myoviridae
DNA Nucleotidyltransferases
DNA-Binding Proteins
Viral Proteins
DNA, Viral
Recombination, Genetic
Binding Sites
Protein Binding
Attachment Sites, Microbiological
Promoter Regions, Genetic
Rights: © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
DOI: 10.1093/nar/gkaa655
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Appears in Collections:Aurora harvest 4
Biochemistry publications

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