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How p53 Molecules Solve the Target DNA Search Problem: A Review

Kamagata, Kiyoto, Itoh, Yuji, Subekti, Dwiky Rendra Graha·2020·International Journal of Molecular Sciences
DOI 10.3390/ijms21031031PMC PMC7037437
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Abstract

Interactions between DNA and DNA-binding proteins play an important role in many essential cellular processes. A key function of the DNA-binding protein p53 is to search for and bind to target sites incorporated in genomic DNA, which triggers transcriptional regulation. How do p53 molecules achieve “rapid” and “accurate” target search in living cells? The search dynamics of p53 were expected to include 3D diffusion in solution, 1D diffusion along DNA, and intersegmental transfer between two different DNA strands. Single-molecule fluorescence microscopy enabled the tracking of p53 molecules on DNA and the characterization of these dynamics quantitatively. Recent intensive single-molecule studies of p53 succeeded in revealing each of these search dynamics. Here, we review these studies and discuss the target search mechanisms of p53.

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Figure 1 Domain organization and function of p53. Thin and thick boxes represent disordered and folded regions, respectively. NT, core, Tet, and CT function as transcriptional regulation, target DNA sequence binding, dimer or tetramer formation, and non-target DNA sequence binding, respectively.
Figure 1 Domain organization and function of p53. Thin and thick boxes represent disordered and folded regions, respectively. NT, core, Tet, and CT function as transcriptional regulation, target DNA sequence binding, dimer or tetramer formation, and non-target DNA sequence binding, respectively.CC BY · PubMed Central
Figure 2 Schematic diagram of representative single-molecule fluorescence microscopy. The system comprises a fluorescence microscope and a flow cell. Fluorescently labeled p53 is introduced into the flow cell using a syringe pump. DNA is tethered on one end to the MPC-polymer-coated glass surface of the flow cell in a line using the DNA garden method. The tethered DNA molecules are stretched by flow pressure. TIRF or HILO is used to illuminate DNA-bound p53 molecules. Fluorescence from the p53 molecules is detected by EM-CCD. The figure is adapted from ref. [25] with some modifications.
Figure 2 Schematic diagram of representative single-molecule fluorescence microscopy. The system comprises a fluorescence microscope and a flow cell. Fluorescently labeled p53 is introduced into the flow cell using a syringe pump. DNA is tethered on one end to the MPC-polymer-coated glass surface of the flow cell in a line using the DNA garden method. The tethered DNA molecules are stretched by flow pressure. TIRF or HILO is used to illuminate DNA-bound p53 molecules. Fluorescence from the p53 molecules is detected by EM-CCD. The figure is adapted from ref. [25] with some modifications.CC BY · PubMed Central
Figure 3 Schematic diagram of the p53-DNA complex structure in 1D diffusion along a non-target DNA sequence. The linker (purple) recruits the core domain (green) to DNA (grey), triggering the conformational switch between fast and slow 1D diffusion modes. The color of p53 domains is the same in Figure 1.
Figure 3 Schematic diagram of the p53-DNA complex structure in 1D diffusion along a non-target DNA sequence. The linker (purple) recruits the core domain (green) to DNA (grey), triggering the conformational switch between fast and slow 1D diffusion modes. The color of p53 domains is the same in Figure 1.CC BY · PubMed Central
Figure 4 (a) Schematic diagram of target search by p53 in the cell. p53 (pink spheres) may bypass other DNA-binding proteins (light blue squares) bound to DNA (black lines) using intersegmental transfer. (b) Single-molecule verification of intersegmental transfer of p53 between crisscrossing DNAs (left). The typical data of p53 demonstrating intersegmental transfer (right). (c) Schematic diagram of intersegmental transfer of p53. p53 binds to the first DNA mainly using the CT domain (Left), grabs the second DNA (Middle), and then releases the former while maintaining contact with the latter DNA (Right). The panels (a) and (c) are adapted from ref. [25] with some modifications, and the panel (b) is adapted from ref. [41] with some modifications.
Figure 4 (a) Schematic diagram of target search by p53 in the cell. p53 (pink spheres) may bypass other DNA-binding proteins (light blue squares) bound to DNA (black lines) using intersegmental transfer. (b) Single-molecule verification of intersegmental transfer of p53 between crisscrossing DNAs (left). The typical data of p53 demonstrating intersegmental transfer (right). (c) Schematic diagram of intersegmental transfer of p53. p53 binds to the first DNA mainly using the CT domain (Left), grabs the second DNA (Middle), and then releases the former while maintaining contact with the latter DNA (Right). The panels (a) and (c) are adapted from ref. [25] with some modifications, and the panel (b) is adapted from ref. [41] with some modifications.CC BY · PubMed Central

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Metadata

Authors
Kamagata, K., Itoh, Y., & Subekti, D. R. G.
Venue
International Journal of Molecular Sciences
Publisher
MDPI AG
Published
2020-02-04
Volume
21
Issue
3
Pages
1031
ISSN
1422-0067
DOI
10.3390/ijms21031031
PMC
PMC7037437
Cited by
29
References
1
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)

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