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Plant coilin: structural characteristics and RNA-binding properties.

Makarov V, Rakitina D, Protopopova A, Yaminsky I, Arutiunian A, Love AJ, Taliansky M, Kalinina N - PLoS ONE (2013)

Bottom Line: Atcoilin is able to bind RNA effectively and in a non-specific manner.The interaction with RNA and subsequent multimerization may facilitate coilin's function as a scaffolding protein.A model of the N-terminal domain is also proposed.

View Article: PubMed Central - PubMed

Affiliation: A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.

ABSTRACT
Cajal bodies (CBs) are dynamic subnuclear compartments involved in the biogenesis of ribonucleoproteins. Coilin is a major structural scaffolding protein necessary for CB formation, composition and activity. The predicted secondary structure of Arabidopsis thaliana coilin (Atcoilin) suggests that the protein is composed of three main domains. Analysis of the physical properties of deletion mutants indicates that Atcoilin might consist of an N-terminal globular domain, a central highly disordered domain and a C-terminal domain containing a presumable Tudor-like structure adjacent to a disordered C terminus. Despite the low homology in amino acid sequences, a similar type of domain organization is likely shared by human and animal coilin proteins and coilin-like proteins of various plant species. Atcoilin is able to bind RNA effectively and in a non-specific manner. This activity is provided by three RNA-binding sites: two sets of basic amino acids in the N-terminal domain and one set in the central domain. Interaction with RNA induces the multimerization of the Atcoilin molecule, a consequence of the structural alterations in the N-terminal domain. The interaction with RNA and subsequent multimerization may facilitate coilin's function as a scaffolding protein. A model of the N-terminal domain is also proposed.

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Effect of U1 snRNA on Atcoilin multimerization.(A) Effect of U1 snRNA on the structure and packing density of Atcoilin and its RNA-binding domains, determined via tryptophan fluorescence, the intensity of which is given in relative units. (B), (C), The hydrodynamic radii of (B) coilin and (C) NOD as free proteins or in complex with U1 snRNA, as elucidated by the DLS method. (D) Atomic-force microscopy of coilin as a free protein (left panels) or in complex with U1 snRNA (right panels). The topographic images of the particles were obtained on the AFM microscope (Nanoscope III) using a contact mode discontinuous with the sample surface. Indicated frame sizes are 1.5×1.5 and 0.6×0.6 µm.
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pone-0053571-g005: Effect of U1 snRNA on Atcoilin multimerization.(A) Effect of U1 snRNA on the structure and packing density of Atcoilin and its RNA-binding domains, determined via tryptophan fluorescence, the intensity of which is given in relative units. (B), (C), The hydrodynamic radii of (B) coilin and (C) NOD as free proteins or in complex with U1 snRNA, as elucidated by the DLS method. (D) Atomic-force microscopy of coilin as a free protein (left panels) or in complex with U1 snRNA (right panels). The topographic images of the particles were obtained on the AFM microscope (Nanoscope III) using a contact mode discontinuous with the sample surface. Indicated frame sizes are 1.5×1.5 and 0.6×0.6 µm.

Mentions: We have assessed the effect of RNA binding on Atcoilin structure and multimerization. Using tryptophan fluorescence we have demonstrated that the addition of U1 snRNA to wt Atcoilin alters its protein structure, such that the emission peak of tryptophan fluorescence is shifted from 347nm to the more hydrophobic 340 nm after complexing RNA (Figure 5A). A similar effect is observed for the NOD, as its peak is shifted to 336 nm, which suggests an increase in the hydrophobicity of the tryptophan local environment (Figure 5A, Table 2). In comparison, the interaction of IDD with RNA does not influence the position of its fluorescence peak (Figure 5A). Fluorescent peak intensity of the full-length Atcoilin and both NOD and IDD domains decreases upon RNA interaction indicating the occurrence of some RNA mediated conformational changes in the protein molecule. Since the changes in peak intensity are maximal in the case of NOD, but much less significant in the case of IDD, it suggests that the modulation of the coilin structure may be predominantly due to the NOD conformational change.


Plant coilin: structural characteristics and RNA-binding properties.

Makarov V, Rakitina D, Protopopova A, Yaminsky I, Arutiunian A, Love AJ, Taliansky M, Kalinina N - PLoS ONE (2013)

Effect of U1 snRNA on Atcoilin multimerization.(A) Effect of U1 snRNA on the structure and packing density of Atcoilin and its RNA-binding domains, determined via tryptophan fluorescence, the intensity of which is given in relative units. (B), (C), The hydrodynamic radii of (B) coilin and (C) NOD as free proteins or in complex with U1 snRNA, as elucidated by the DLS method. (D) Atomic-force microscopy of coilin as a free protein (left panels) or in complex with U1 snRNA (right panels). The topographic images of the particles were obtained on the AFM microscope (Nanoscope III) using a contact mode discontinuous with the sample surface. Indicated frame sizes are 1.5×1.5 and 0.6×0.6 µm.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3539977&req=5

pone-0053571-g005: Effect of U1 snRNA on Atcoilin multimerization.(A) Effect of U1 snRNA on the structure and packing density of Atcoilin and its RNA-binding domains, determined via tryptophan fluorescence, the intensity of which is given in relative units. (B), (C), The hydrodynamic radii of (B) coilin and (C) NOD as free proteins or in complex with U1 snRNA, as elucidated by the DLS method. (D) Atomic-force microscopy of coilin as a free protein (left panels) or in complex with U1 snRNA (right panels). The topographic images of the particles were obtained on the AFM microscope (Nanoscope III) using a contact mode discontinuous with the sample surface. Indicated frame sizes are 1.5×1.5 and 0.6×0.6 µm.
Mentions: We have assessed the effect of RNA binding on Atcoilin structure and multimerization. Using tryptophan fluorescence we have demonstrated that the addition of U1 snRNA to wt Atcoilin alters its protein structure, such that the emission peak of tryptophan fluorescence is shifted from 347nm to the more hydrophobic 340 nm after complexing RNA (Figure 5A). A similar effect is observed for the NOD, as its peak is shifted to 336 nm, which suggests an increase in the hydrophobicity of the tryptophan local environment (Figure 5A, Table 2). In comparison, the interaction of IDD with RNA does not influence the position of its fluorescence peak (Figure 5A). Fluorescent peak intensity of the full-length Atcoilin and both NOD and IDD domains decreases upon RNA interaction indicating the occurrence of some RNA mediated conformational changes in the protein molecule. Since the changes in peak intensity are maximal in the case of NOD, but much less significant in the case of IDD, it suggests that the modulation of the coilin structure may be predominantly due to the NOD conformational change.

Bottom Line: Atcoilin is able to bind RNA effectively and in a non-specific manner.The interaction with RNA and subsequent multimerization may facilitate coilin's function as a scaffolding protein.A model of the N-terminal domain is also proposed.

View Article: PubMed Central - PubMed

Affiliation: A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.

ABSTRACT
Cajal bodies (CBs) are dynamic subnuclear compartments involved in the biogenesis of ribonucleoproteins. Coilin is a major structural scaffolding protein necessary for CB formation, composition and activity. The predicted secondary structure of Arabidopsis thaliana coilin (Atcoilin) suggests that the protein is composed of three main domains. Analysis of the physical properties of deletion mutants indicates that Atcoilin might consist of an N-terminal globular domain, a central highly disordered domain and a C-terminal domain containing a presumable Tudor-like structure adjacent to a disordered C terminus. Despite the low homology in amino acid sequences, a similar type of domain organization is likely shared by human and animal coilin proteins and coilin-like proteins of various plant species. Atcoilin is able to bind RNA effectively and in a non-specific manner. This activity is provided by three RNA-binding sites: two sets of basic amino acids in the N-terminal domain and one set in the central domain. Interaction with RNA induces the multimerization of the Atcoilin molecule, a consequence of the structural alterations in the N-terminal domain. The interaction with RNA and subsequent multimerization may facilitate coilin's function as a scaffolding protein. A model of the N-terminal domain is also proposed.

Show MeSH