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Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function.

Khan F, Daniëls MA, Folkers GE, Boelens R, Saqlan Naqvi SM, van Ingen H - Nucleic Acids Res. (2014)

Bottom Line: A HADDOCK model of the NtRRM-RNA complex, based on NMR chemical shift and NOE data, shows that nucleic acid binding results from a combination of stacking and electrostatic interactions with conserved RRM residues.Finally, DNA melting experiments demonstrate that NtGR-RBP1 is more efficient in melting CTG containing nucleic acids than isolated NtRRM.Together, our study supports the model that self-association of GR-RBPs by the glycine-rich region results in cooperative unfolding of non-native substrate structures, thereby enhancing its chaperone function.

View Article: PubMed Central - PubMed

Affiliation: NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Department of Biochemistry, PMAS Agriculture University Rawalpindi, 46300 Rawalpindi, Pakistan.

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NtGR-RBP1 is highly conserved from bacteria to human. The alignment is generated by CLUSTAL W and displayed by Seaview with colour coding according to amino acid properties. The location of the RNP motifs and the glycine-rich region is indicated. Secondary structure elements as present in the structure of the NtRRM domain of NtGR-RBP1 are indicated below the alignment and labelled as in Figure 2 (orange arrows: β-strand; blue bars: α-helix). Residues that were found to be in the nucleic acid interaction surface are indicated with *. CIRP = cold inducible RNA-binding protein; GR-RBP = glycine-rich RNA-binding protein; RBP = RNA-binding protein.
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Figure 1: NtGR-RBP1 is highly conserved from bacteria to human. The alignment is generated by CLUSTAL W and displayed by Seaview with colour coding according to amino acid properties. The location of the RNP motifs and the glycine-rich region is indicated. Secondary structure elements as present in the structure of the NtRRM domain of NtGR-RBP1 are indicated below the alignment and labelled as in Figure 2 (orange arrows: β-strand; blue bars: α-helix). Residues that were found to be in the nucleic acid interaction surface are indicated with *. CIRP = cold inducible RNA-binding protein; GR-RBP = glycine-rich RNA-binding protein; RBP = RNA-binding protein.

Mentions: Tobacco NtGR-RBP1 is a ∼16 kDa protein comprised of an NtRRM domain (85 residues) followed by a glycine-rich region of roughly the same length. Sequence alignment shows that NtGR-RBP1 is highly conserved with orthologous in Arabidopsis and Zea mays sharing 76% and 73% amino acid identity, respectively, and ∼40% homology to mouse, human and bacterial counterparts (Figure 1). Sequence conservation is highest in the NtRRM domain which features the two canonical RNP motifs that have been shown to be required for RNA binding in other RRM domains (2).


Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function.

Khan F, Daniëls MA, Folkers GE, Boelens R, Saqlan Naqvi SM, van Ingen H - Nucleic Acids Res. (2014)

NtGR-RBP1 is highly conserved from bacteria to human. The alignment is generated by CLUSTAL W and displayed by Seaview with colour coding according to amino acid properties. The location of the RNP motifs and the glycine-rich region is indicated. Secondary structure elements as present in the structure of the NtRRM domain of NtGR-RBP1 are indicated below the alignment and labelled as in Figure 2 (orange arrows: β-strand; blue bars: α-helix). Residues that were found to be in the nucleic acid interaction surface are indicated with *. CIRP = cold inducible RNA-binding protein; GR-RBP = glycine-rich RNA-binding protein; RBP = RNA-binding protein.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4117745&req=5

Figure 1: NtGR-RBP1 is highly conserved from bacteria to human. The alignment is generated by CLUSTAL W and displayed by Seaview with colour coding according to amino acid properties. The location of the RNP motifs and the glycine-rich region is indicated. Secondary structure elements as present in the structure of the NtRRM domain of NtGR-RBP1 are indicated below the alignment and labelled as in Figure 2 (orange arrows: β-strand; blue bars: α-helix). Residues that were found to be in the nucleic acid interaction surface are indicated with *. CIRP = cold inducible RNA-binding protein; GR-RBP = glycine-rich RNA-binding protein; RBP = RNA-binding protein.
Mentions: Tobacco NtGR-RBP1 is a ∼16 kDa protein comprised of an NtRRM domain (85 residues) followed by a glycine-rich region of roughly the same length. Sequence alignment shows that NtGR-RBP1 is highly conserved with orthologous in Arabidopsis and Zea mays sharing 76% and 73% amino acid identity, respectively, and ∼40% homology to mouse, human and bacterial counterparts (Figure 1). Sequence conservation is highest in the NtRRM domain which features the two canonical RNP motifs that have been shown to be required for RNA binding in other RRM domains (2).

Bottom Line: A HADDOCK model of the NtRRM-RNA complex, based on NMR chemical shift and NOE data, shows that nucleic acid binding results from a combination of stacking and electrostatic interactions with conserved RRM residues.Finally, DNA melting experiments demonstrate that NtGR-RBP1 is more efficient in melting CTG containing nucleic acids than isolated NtRRM.Together, our study supports the model that self-association of GR-RBPs by the glycine-rich region results in cooperative unfolding of non-native substrate structures, thereby enhancing its chaperone function.

View Article: PubMed Central - PubMed

Affiliation: NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Department of Biochemistry, PMAS Agriculture University Rawalpindi, 46300 Rawalpindi, Pakistan.

Show MeSH
Related in: MedlinePlus