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Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring.

Lu C, Ding F, Ke A - PLoS ONE (2010)

Bottom Line: In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry.Since increased conformational flexibility was also observed in the RNA-binding ring of the related bacterial PNPase, we speculate that this may reflect an evolutionarily conserved mechanism to accommodate diverse RNA substrates for degradation.This study clearly shows the dynamic structures within the RNA-binding domains, which provides additional insights on mechanism of asymmetric RNA binding and processing.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.

ABSTRACT

Background: The exosome complex is an essential RNA 3'-end processing and degradation machinery. In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry.

Methodology/principal findings: Here we report an asymmetric 2.9 A Sulfolobus solfataricus archaeal exosome structure in which the three-fold symmetry is broken due to combined rigid body and thermal motions mainly within the RNA-binding ring. Since increased conformational flexibility was also observed in the RNA-binding ring of the related bacterial PNPase, we speculate that this may reflect an evolutionarily conserved mechanism to accommodate diverse RNA substrates for degradation.

Conclusion/significance: This study clearly shows the dynamic structures within the RNA-binding domains, which provides additional insights on mechanism of asymmetric RNA binding and processing.

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Related in: MedlinePlus

Detecting thermal motions in Rrp4 RNA-binding ring using thermal ellipsoid and B-factor analyses.(a) Overall analysis of the trimeric cap. (b) According to the thermal ellipsoid analysis, the most thermal flexible Rrp4 subunit is Chain I, but not Chain F, which displays the largest rigidbody motion. TLS sensors were obtained from TLS refinement in Refmac5 [48] (see Methods section for details) and plotted using Raster3D [51].(c) B-factor comparison of the Rrp4 between our S. solfataricus exosome (left) and that Lorentzen et al previously reported [30] (right). B-factor coloring: blue, 30 and below; red, 100 and above.
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pone-0008739-g004: Detecting thermal motions in Rrp4 RNA-binding ring using thermal ellipsoid and B-factor analyses.(a) Overall analysis of the trimeric cap. (b) According to the thermal ellipsoid analysis, the most thermal flexible Rrp4 subunit is Chain I, but not Chain F, which displays the largest rigidbody motion. TLS sensors were obtained from TLS refinement in Refmac5 [48] (see Methods section for details) and plotted using Raster3D [51].(c) B-factor comparison of the Rrp4 between our S. solfataricus exosome (left) and that Lorentzen et al previously reported [30] (right). B-factor coloring: blue, 30 and below; red, 100 and above.

Mentions: Besides conformational heterogeneity caused by the hinge motion, the Rrp4 trimer also exhibits distinct temperature factor distributions, which reflect the RNA binding ring's inherent conformational flexibilities. TLS refinement followed by thermal ellipsoids analysis revealed unique thermal motions in Chain I copy of Rrp4 (Fig. 4a, b). Although Chain C and Chain I of Rrp4 adopt very similar conformations, Chain I displays considerably higher thermal motion than Chain C, manifested by a higher average temperature factor of 81 versus 61 (Fig. 4a, c), as well as wider thermal ellipsoids in Chain I (Fig. 4b). Each Rrp4 subunit has distinct temperature factor distributions within the polypeptide (Fig. 4a, c). The shape of the thermal ellipsoids revealed that Chain I wobbles to a larger extent on top of the catalytic ring, and in a concentric motion relative to the central RNA-processing chamber. All above observations indicate that the Rrp4 trimeric cap is intrinsically flexible, despite bound to the relatively rigid catalytic ring. The observed conformational heterogeneity agrees perfectly with the function of the RNA-binding ring of the exosome to accommodate diverse RNA substrates.


Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring.

Lu C, Ding F, Ke A - PLoS ONE (2010)

Detecting thermal motions in Rrp4 RNA-binding ring using thermal ellipsoid and B-factor analyses.(a) Overall analysis of the trimeric cap. (b) According to the thermal ellipsoid analysis, the most thermal flexible Rrp4 subunit is Chain I, but not Chain F, which displays the largest rigidbody motion. TLS sensors were obtained from TLS refinement in Refmac5 [48] (see Methods section for details) and plotted using Raster3D [51].(c) B-factor comparison of the Rrp4 between our S. solfataricus exosome (left) and that Lorentzen et al previously reported [30] (right). B-factor coloring: blue, 30 and below; red, 100 and above.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2806925&req=5

pone-0008739-g004: Detecting thermal motions in Rrp4 RNA-binding ring using thermal ellipsoid and B-factor analyses.(a) Overall analysis of the trimeric cap. (b) According to the thermal ellipsoid analysis, the most thermal flexible Rrp4 subunit is Chain I, but not Chain F, which displays the largest rigidbody motion. TLS sensors were obtained from TLS refinement in Refmac5 [48] (see Methods section for details) and plotted using Raster3D [51].(c) B-factor comparison of the Rrp4 between our S. solfataricus exosome (left) and that Lorentzen et al previously reported [30] (right). B-factor coloring: blue, 30 and below; red, 100 and above.
Mentions: Besides conformational heterogeneity caused by the hinge motion, the Rrp4 trimer also exhibits distinct temperature factor distributions, which reflect the RNA binding ring's inherent conformational flexibilities. TLS refinement followed by thermal ellipsoids analysis revealed unique thermal motions in Chain I copy of Rrp4 (Fig. 4a, b). Although Chain C and Chain I of Rrp4 adopt very similar conformations, Chain I displays considerably higher thermal motion than Chain C, manifested by a higher average temperature factor of 81 versus 61 (Fig. 4a, c), as well as wider thermal ellipsoids in Chain I (Fig. 4b). Each Rrp4 subunit has distinct temperature factor distributions within the polypeptide (Fig. 4a, c). The shape of the thermal ellipsoids revealed that Chain I wobbles to a larger extent on top of the catalytic ring, and in a concentric motion relative to the central RNA-processing chamber. All above observations indicate that the Rrp4 trimeric cap is intrinsically flexible, despite bound to the relatively rigid catalytic ring. The observed conformational heterogeneity agrees perfectly with the function of the RNA-binding ring of the exosome to accommodate diverse RNA substrates.

Bottom Line: In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry.Since increased conformational flexibility was also observed in the RNA-binding ring of the related bacterial PNPase, we speculate that this may reflect an evolutionarily conserved mechanism to accommodate diverse RNA substrates for degradation.This study clearly shows the dynamic structures within the RNA-binding domains, which provides additional insights on mechanism of asymmetric RNA binding and processing.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.

ABSTRACT

Background: The exosome complex is an essential RNA 3'-end processing and degradation machinery. In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry.

Methodology/principal findings: Here we report an asymmetric 2.9 A Sulfolobus solfataricus archaeal exosome structure in which the three-fold symmetry is broken due to combined rigid body and thermal motions mainly within the RNA-binding ring. Since increased conformational flexibility was also observed in the RNA-binding ring of the related bacterial PNPase, we speculate that this may reflect an evolutionarily conserved mechanism to accommodate diverse RNA substrates for degradation.

Conclusion/significance: This study clearly shows the dynamic structures within the RNA-binding domains, which provides additional insights on mechanism of asymmetric RNA binding and processing.

Show MeSH
Related in: MedlinePlus