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Functional interplay between the RK motif and linker segment dictates Oct4-DNA recognition.

Kong X, Liu J, Li L, Yue L, Zhang L, Jiang H, Xie X, Luo C - Nucleic Acids Res. (2015)

Bottom Line: Intriguingly, computational simulations reveal that the function of the RK motif may be finely tuned by H-bond interactions with the partially disordered linker segment and that breaking these interactions significantly enhances the DNA binding and reprogramming activities of Oct4.These findings uncover a self-regulatory mechanism for specific Oct4-DNA recognition and provide insights into the functional crosstalk at the molecular level that may illuminate mechanistic studies of the Oct protein family and possibly transcription factors in the POU family.Our gain-of-function Oct4 mutants might also be useful tools for use in reprogramming and regenerative medicine.

View Article: PubMed Central - PubMed

Affiliation: Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

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A model for the role of the interaction between the RK motif (yellow) and linker segment (purple) in specific DNA recognition by Oct4. The POUs subdomain is coloured green, and the POUh subdomain, except the RK-motif, is coloured cyan. The enhanced minor groove electrostatic potential at the narrowed minor groove is highlighted in red.
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Figure 5: A model for the role of the interaction between the RK motif (yellow) and linker segment (purple) in specific DNA recognition by Oct4. The POUs subdomain is coloured green, and the POUh subdomain, except the RK-motif, is coloured cyan. The enhanced minor groove electrostatic potential at the narrowed minor groove is highlighted in red.

Mentions: Based on the aforementioned results, we propose the following model for the functional interplay of the RK-motif and linker segment in Oct4–DNA binding (Figure 5). The dynamic and solvent-accessible RK-motif is essential to Oct4–DNA recognition through the perception of the enhanced electronegative potential and other important physicochemical properties, such as the specific hydration and hydrophobic environment in the narrowed minor groove. The H-bond interactions between the negatively charged glutamic acid residues in the linker segment and RK-motif may help to prevent the non-specific interactions of RK-motif with the random DNA sequences in genome. Upon associating with potential Oct4 binding sites containing A-tracts, the attractions from the enhanced minor groove electronegative potential may acts as a counterbalance to the H-bond interactions from the linker segment and help the release of the RK-motif for minor groove recognition. The similar situations were observed for other transcription factors, such as the ultrabithorax (Ubx) protein, in which the intramolecular interactions of disordered segments (I1, I2 and R region) and homeodomain constraint the non-specific interactions of homeodomain and thus increase its DNA binding specificity. (59,60) Moreover, the post-translational modifications (PTM) of the disordered region can modulate the DNA binding activities by intramolecular interactions with the binding determinants in some protein–DNA complexes. (61,62) It is thus speculated that the PTM in the linker segment of Oct4, such as the phosphorylation of serine or threonine, may affect its interplay with the RK-motif and thus the reprogramming efficiency. Correspondingly, albeit no data has been reported now, the potential PTMs or PPI with other regulatory factors of the solvent accessible RK-motif might achieve the similar effects.


Functional interplay between the RK motif and linker segment dictates Oct4-DNA recognition.

Kong X, Liu J, Li L, Yue L, Zhang L, Jiang H, Xie X, Luo C - Nucleic Acids Res. (2015)

A model for the role of the interaction between the RK motif (yellow) and linker segment (purple) in specific DNA recognition by Oct4. The POUs subdomain is coloured green, and the POUh subdomain, except the RK-motif, is coloured cyan. The enhanced minor groove electrostatic potential at the narrowed minor groove is highlighted in red.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482079&req=5

Figure 5: A model for the role of the interaction between the RK motif (yellow) and linker segment (purple) in specific DNA recognition by Oct4. The POUs subdomain is coloured green, and the POUh subdomain, except the RK-motif, is coloured cyan. The enhanced minor groove electrostatic potential at the narrowed minor groove is highlighted in red.
Mentions: Based on the aforementioned results, we propose the following model for the functional interplay of the RK-motif and linker segment in Oct4–DNA binding (Figure 5). The dynamic and solvent-accessible RK-motif is essential to Oct4–DNA recognition through the perception of the enhanced electronegative potential and other important physicochemical properties, such as the specific hydration and hydrophobic environment in the narrowed minor groove. The H-bond interactions between the negatively charged glutamic acid residues in the linker segment and RK-motif may help to prevent the non-specific interactions of RK-motif with the random DNA sequences in genome. Upon associating with potential Oct4 binding sites containing A-tracts, the attractions from the enhanced minor groove electronegative potential may acts as a counterbalance to the H-bond interactions from the linker segment and help the release of the RK-motif for minor groove recognition. The similar situations were observed for other transcription factors, such as the ultrabithorax (Ubx) protein, in which the intramolecular interactions of disordered segments (I1, I2 and R region) and homeodomain constraint the non-specific interactions of homeodomain and thus increase its DNA binding specificity. (59,60) Moreover, the post-translational modifications (PTM) of the disordered region can modulate the DNA binding activities by intramolecular interactions with the binding determinants in some protein–DNA complexes. (61,62) It is thus speculated that the PTM in the linker segment of Oct4, such as the phosphorylation of serine or threonine, may affect its interplay with the RK-motif and thus the reprogramming efficiency. Correspondingly, albeit no data has been reported now, the potential PTMs or PPI with other regulatory factors of the solvent accessible RK-motif might achieve the similar effects.

Bottom Line: Intriguingly, computational simulations reveal that the function of the RK motif may be finely tuned by H-bond interactions with the partially disordered linker segment and that breaking these interactions significantly enhances the DNA binding and reprogramming activities of Oct4.These findings uncover a self-regulatory mechanism for specific Oct4-DNA recognition and provide insights into the functional crosstalk at the molecular level that may illuminate mechanistic studies of the Oct protein family and possibly transcription factors in the POU family.Our gain-of-function Oct4 mutants might also be useful tools for use in reprogramming and regenerative medicine.

View Article: PubMed Central - PubMed

Affiliation: Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

Show MeSH
Related in: MedlinePlus