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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

Purification and activity assay of the purified S. solfataricus full exosome.(a) SDS-PAGE of the purified S. solfataricus full exosome (left) and the Rrp4-exosome isoform (right). (b) RNase activity assay for the intact S. solfataricus exosome. The exosome is stalled by the HDV ribozyme sequence. (c) Side and top-down view of the 2.9 Å S. solfataricus exosome structure. Gold, trimeric Rrp4 RNA-binding ring; blue/cyan, Rrp41/Rrp42 catalytic ring.
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pone-0008739-g001: Purification and activity assay of the purified S. solfataricus full exosome.(a) SDS-PAGE of the purified S. solfataricus full exosome (left) and the Rrp4-exosome isoform (right). (b) RNase activity assay for the intact S. solfataricus exosome. The exosome is stalled by the HDV ribozyme sequence. (c) Side and top-down view of the 2.9 Å S. solfataricus exosome structure. Gold, trimeric Rrp4 RNA-binding ring; blue/cyan, Rrp41/Rrp42 catalytic ring.

Mentions: When we started the work, studies had shown that all four eukaryotic exosome homologous proteins, namely Rrp41, Rrp42, Rrp4, and Csl4, are present in the purified archaeal exosome complex [31], [34], [35], [36], [37], [38]. We therefore attempted to reconstitute the archaeal Sulfolobus solfataricus exosome by co-expressing all four exosome subunits from a polycistronic construct in E. coli [39], [40], [41]. As shown in the results, while Rrp4, Rrp41, and Rrp42 were present at stoichiometric amounts in the purified complex, the Csl4 protein appeared sub-stoichiometric (Fig. 1a). The purified exosome complex was shown to be monodispersed and homogeneous under negative staining EM (data not shown).


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)

Purification and activity assay of the purified S. solfataricus full exosome.(a) SDS-PAGE of the purified S. solfataricus full exosome (left) and the Rrp4-exosome isoform (right). (b) RNase activity assay for the intact S. solfataricus exosome. The exosome is stalled by the HDV ribozyme sequence. (c) Side and top-down view of the 2.9 Å S. solfataricus exosome structure. Gold, trimeric Rrp4 RNA-binding ring; blue/cyan, Rrp41/Rrp42 catalytic ring.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0008739-g001: Purification and activity assay of the purified S. solfataricus full exosome.(a) SDS-PAGE of the purified S. solfataricus full exosome (left) and the Rrp4-exosome isoform (right). (b) RNase activity assay for the intact S. solfataricus exosome. The exosome is stalled by the HDV ribozyme sequence. (c) Side and top-down view of the 2.9 Å S. solfataricus exosome structure. Gold, trimeric Rrp4 RNA-binding ring; blue/cyan, Rrp41/Rrp42 catalytic ring.
Mentions: When we started the work, studies had shown that all four eukaryotic exosome homologous proteins, namely Rrp41, Rrp42, Rrp4, and Csl4, are present in the purified archaeal exosome complex [31], [34], [35], [36], [37], [38]. We therefore attempted to reconstitute the archaeal Sulfolobus solfataricus exosome by co-expressing all four exosome subunits from a polycistronic construct in E. coli [39], [40], [41]. As shown in the results, while Rrp4, Rrp41, and Rrp42 were present at stoichiometric amounts in the purified complex, the Csl4 protein appeared sub-stoichiometric (Fig. 1a). The purified exosome complex was shown to be monodispersed and homogeneous under negative staining EM (data not shown).

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