Abstract
Localized arrays of proteins cooperatively assemble onto chromosomes to control DNA activity in many contexts. Binding cooperativity is often mediated by specific protein–protein interactions, but cooperativity through DNA structure is becoming increasingly recognized as an additional mechanism. During the site-specific DNA recombination reaction that excises phage λ from the chromosome, the bacterial DNA architectural protein Fis recruits multiple λ-encoded Xis proteins to the attR recombination site. Here, we report X-ray crystal structures of DNA complexes containing Fis + Xis, which show little, if any, contacts between the two proteins. Comparisons with structures of DNA complexes containing only Fis or Xis, together with mutant protein and DNA binding studies, support a mechanism for cooperative protein binding solely by DNA allostery. Fis binding both molds the minor groove to potentiate insertion of the Xis β-hairpin wing motif and bends the DNA to facilitate Xis-DNA contacts within the major groove. The Fis-structured minor groove shape that is optimized for Xis binding requires a precisely positioned pyrimidine-purine base-pair step, whose location has been shown to modulate minor groove widths in Fis-bound complexes to different DNA targets.
Highlights
Cooperative interactions between DNA-binding proteins at specific genomic sites govern many cellular processes including transcription, replication, and recombination
We focus on the ability of the Escherichia coli Fis protein to recruit the phage-encoded Xis protein to the attR recombination site, a key control step in formation of the excisive intasome (Figure 1B) [4,5]
The structure of the Xis bound over X1 in the FX1-2-2Xis complex is not relevant to Fis–Xis cooperativity, we discuss below how it informs on Xis–Xis interactions leading to formation of the Xis nucleoprotein filament and why Xis bound to the X1 sequence in the correct configuration was not obtained
Summary
Cooperative interactions between DNA-binding proteins at specific genomic sites govern many cellular processes including transcription, replication, and recombination. Most reported instances of binding cooperativity on DNA involve direct protein–protein interactions, but there are examples whereby local protein-induced changes in DNA structure have been implicated in promoting binding of partner proteins. By this mechanism, binding of one protein to a specific site changes DNA shape so as to create an optimized DNA conformation for a second protein that would otherwise exhibit poorer binding affinity to that site. An often cited example is the cooperative binding of eight different transcription factors within a 55 bp segment of the interferon- enhanceosome, where X-ray crystallography revealed few direct protein–protein interactions between binding partners [1]. Evidence has been presented indicating that conformational features of DNA can be transmitted over distances of one or two helical turns to influence binding kinetics of different protein pairs [2]
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