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Review
. 2018 Apr 17;51(4):860-868.
doi: 10.1021/acs.accounts.7b00541. Epub 2018 Jan 25.

Facilitated Unbinding via Multivalency-Enabled Ternary Complexes: New Paradigm for Protein-DNA Interactions

Affiliations
Review

Facilitated Unbinding via Multivalency-Enabled Ternary Complexes: New Paradigm for Protein-DNA Interactions

Tai-Yen Chen et al. Acc Chem Res. .

Abstract

Dynamic protein-DNA interactions constitute highly robust cellular machineries to fulfill cellular functions. A vast number of studies have focused on how DNA-binding proteins search for and interact with their target DNA segments and on what cellular cues can regulate protein binding, for which protein concentration is a most obvious one. In contrast, how protein unbinding could be regulated by protein concentration has evaded attention because protein unbinding from DNA is typically a unimolecular reaction and thus concentration independent. Recent single-molecule studies from multiple research groups have uncovered that protein concentration can facilitate the unbinding of DNA-bound proteins, revealing regulation of protein unbinding as another mechanistic paradigm for gene regulation. In this Account, we review these recent in vitro and in vivo single-molecule experiments that uncovered the concentration-facilitated protein unbinding by multiple types of DNA-binding proteins, including sequence-nonspecific DNA-binding proteins (e.g., nucleoid-associated proteins, NAP), sequence-specific DNA-binding proteins (e.g., metal-responsive transcription regulators CueR and ZntR), sequence-neutral single-stranded DNA-binding proteins (e.g., Replication protein A, RPA), and DNA polymerases. For the in vitro experiments, Marko's group investigated the exchange of GFP-tagged DNA-bound NAPs with nontagged NAPs in solution of increasing concentration using single-molecule magnetic-tweezers fluorescence microscopy. The faster fluorescence intensity decrease with higher nontagged NAP concentrations suggests that DNA-bound NAPs undergo faster exchange with higher free NAP concentrations. Chen's group used single-molecule fluorescence resonance energy transfer measurements to study the unbinding of CueR from its cognate oligomeric DNA. The average microscopic dwell times of DNA-bound states become shorter with increasing CueR concentrations in the surroundings, demonstrating that free CueR proteins can facilitate the unbinding of the incumbent one on DNA through either assisted dissociation or direct substitution. Greene's group studied the unbinding of RPAs from single-stranded DNA using total internal reflection fluorescence microscopy and DNA curtain techniques. The fluorescence intensity versus time traces show faster decay with higher wild-type RPA concentrations, indicating that DNA-bound RPAs can undergo a concentration-facilitated exchange when encountering excess free RPA. van Oijen's group investigated the leading/lagging-strand polymerase exchange events in the bacteriophage T7 and E. coli replication systems using a combination of single-molecule fluorescence microscopy and DNA-flow-stretching assay. The processivity was observed to have larger decrease when the concentration of the Y526F polymerase mutant increases, indicating that the unbinding of the polymerase is also concentration-dependent. Using stroboscopic imaging and single-molecule tracking, Chen's group further advanced their study into living bacterial cells. They found CueR, as well as its homologue ZntR, shows concentration-enhanced unbinding from its DNA-binding site in vivo. Mechanistic consensus has emerged from these in vitro and in vivo single-molecule studies that encompass a range of proteins with distinct biological functions. It involves multivalent contacts between protein and DNA. The multivalency enables the formation of ternary complexes as intermediates, which subsequently give rise to concentration-enhanced protein unbinding. As multivalent contacts are ubiquitous among DNA-interacting proteins, this multivalency-enabled facilitated unbinding mechanism thus provides a potentially general mechanistic paradigm in regulating protein-DNA interactions.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

Figure 1
Figure 1
(a) NAPs interact with bacterial chromosome and shape the DNA structure for different functions. (b) Experimental configuration of the single-molecule magnetic-tweezers-fluorescence microscope. (c) Experimental results of the Fis exchange assays. The intensity decay is due to the replacement of the pre-bound GFP-Fis on DNA by the WT-Fis in solution. The intensity versus time trajectories indicate that the Fis exchange rate gets faster with higher concentrations of WT-Fis. (d) Schematic mechanism for the facilitated unbinding process. Panels b and c reproduced with permission from Reference. Copyright 2010 Oxford University Press. Panel d reproduced with permission from Reference. Copyright 2015 Elsevier Ltd.
Figure 2
Figure 2
(a) DNA-distortion mechanism of CueR. Apo- and holo-CueR bind to DNA to repress and activate the transcription of metal-defense genes. (b) SmFRET experimental design to study the binding and unbinding events between CueR molecules and DNA. (c) (Upper) single-molecule EFRET trajectory of an immobilized Cy3-DNA interacting with Cy5-labeled apo-CueR shows three EFRET states and microscopic dwell times of each state. (Lower) same as the upper panel but Cy3-DNA interacts with a mixture of Cy5-labeled apo-CueR and holo-CueR, in which Cy5 on holo-CueR is at a different location from that of apo-CueR. The blue arrows denote the transitions from the holo-protein-bound states to the apo-protein-bound states, and the black arrows denote the reverse transitions; these transitions report the direct substitution of a DNA-bound holo-protein by an apo-protein or the reverse. (d) The average dwell time (〈τ2〉) gets shorter with increasing [CueR], reflecting the direct-substitution and assisted-dissociation pathways of CueR-DNA interactions. (e) Proposed mechanism involving a ternary CueR2-DNA complex as an intermediate for direct-substitution and assisted-dissociation pathways to a CueR bound at a specific DNA-binding site. Reproduced with permission from Reference and reference. Copyright 2013 American Chemical Society and 2012 National Academy of Sciences.
Figure 3
Figure 3
(a) Schematic representation of RPA’s function in DNA replication (left) and recombination (right). (b) Experimental device for a double-tethered DNA-curtain assay. (c) The kymograph (upper) and intensity-versus-time traces of eGFP-RPA under various WT-RPA concentrations (lower). The fluorescent signals of eGFP-RPA decreased with time when WT-RPA was adding to the flow cell. The concentration-dependent-RPA-exchange rate reflects a facilitated dissociation (or exchange) behavior. (d) Schematic depiction of the microscopic dissociation mechanism for the facilitated-dissociation/exchange phenomenon of RPA. Panel b reproduced with permission from Reference. Copyright 2012 National Academy of Sciences. Panel c and d reproduced with permission from Reference. Copyright 2014 Public Library of Science.
Figure 4
Figure 4
(a) Schematic diagram and components for the bacteriophage T7 replication system. (b) Experimental design for examining the polymerase exchange during leading strand DNA synthesis. The DNA synthesis rate was calculated by the movement of QD within a given time window. (c) WT and mutant (Y526F) polymerases possess different DNA synthesis rates demonstrated by different slopes in blue and red trajectories (left). The processivity is calculated from the leading-strand DNA synthesis. Results from various mutant concentrations give the titration curve on the right. (d) Experimental design for studying the polymerase exchange during lagging-strand DNA synthesis (upper). Fluctuations in intensity-versus-time trajectory represent polymerase exchange events between different fluorophores (blue and red) (lower). (e) DNA polymerase binds the DNA template (primary binding site) and helicase (secondary binding site). The partial-dissociation state allows free polymerase filling in the opened binding site and consequently displacing the original polymerase. (f) in vitro fluorescence intensity of Pol III* was monitoring with a periodic high laser power pulse (upper). The normalized intensity after pulse was plotted as a function of time with four Pol III* concentrations (lower). Panels a–d reproduced with permission from Reference,,. Copyright 2007, 2011 and 2014 National Academy of Sciences. Panel e reproduced with permission from Reference. Copyright 2016 Oxford University Press. Panel f reproduced with permission from Reference. Copyright 2017 eLife Sciences Publications.
Figure 5
Figure 5
(a) Single-molecule tracking (left) using stroboscopic imaging scheme together with super-resolution analysis generates the moving trajectories (right) and displacement (r) trajectory (panel c) in living cells. (b) Histogram of displacement r and the corresponding resolved diffusion states. The black solid line is the overall probability-density-function. Red, green, and blue lines represent the populations of the regulator at the specifically-bound (SB), non-specifically bound (NB), and freely-diffusing (FD) states, respectively. The vertical red dashed line denotes the displacement threshold, r0, to select out microscopic residence time of CueR molecules bound to specific binding sites. (c) Displacement-per-time-lapse-versus-time trajectory for the tracked CueR. τ1 and τ2 are two microscopic residence times (two grey shades) thresholded by r0 (horizontal red dashed line). (d) Dependences of k-1app on free CueR concentration in cells. (e) Proposed transcription regulation processes in live bacteria using the concentration-dependent unbinding mechanism. Panels b–d reproduced with permission from Reference. Copyright 2015 Nature Publishing Group.
Figure 6
Figure 6
General mechanism of protein-concentration-dependent unbinding from DNA.

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