Research Article: Crystal Structure of the S. solfataricus Archaeal Exosome Reveals Conformational Flexibility in the RNA-Binding Ring

Date Published: January 15, 2010

Publisher: Public Library of Science

Author(s): Changrui Lu, Fang Ding, Ailong Ke, Petri Kursula.

Abstract: 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.

Partial Text: The exosome and its related bacterial polynucleotide phosphorylase (PNPase) represent a class of conserved multi-subunit protein complexes responsible for the 3′-to-5′ processing and degradation of RNA [1], [2], [3]. In the nucleus of eukaryotic cells, the exosome is responsible for the 3′-end trimming of rRNA, snRNA, and snoRNA, but also plays a major role in the degradation of the spliced introns and pre-mRNAs that fail the quality control processes [4], [5], [6], [7], [8], [9], [10], [11], [12], [13]. In addition, the nuclear exosome participates in nuclear surveillance pathways to degrade aberrant rRNA, tRNA, and mRNA transcripts [6], [11], [12], [14], [15], [16], [17]. In the cytoplasm, the exosome is a key player during mRNA turnover, and is responsible for the 3′-to-5′ degradation of normal mRNA after deadenylation as well as for the products of endonucleolytic events [18], including those of the RNAi pathway [19]. Like the nuclear exosome, the cytoplasmic exosome also participates in mRNA surveillance pathways such as nonsense-mediated decay, non-stop decay, no-go decay, and ARE-mediated decay to eliminate aberrant mRNAs [20], [21], [22], [23], [24].

Previous structural studies of the archaeal exosome from three different species all reported perfect three-fold symmetric subunit arrangements within this RNA processing machine. An interesting observation from these studies was that the RNA-binding ring displays large conformational differences among different species. For example, the conformation of the S. solfataricus exosome RNA-binding ring differs dramatically from what was seen in the A. fulgidus structure mostly due to rigid body rearrangement of the KH, S1, and NT domain locations [31] (r.m.s.d. of the Cα atom alignment in the 750-aminoacid Rrp4 region is 5.2 Å). This either suggests a faster evolution rate within the RNA-binding part of the exosome, or hints at inherent conformational flexibilities in this region. Through careful analyses of the conformation and thermal motion of each subunit, we provide evidence to support the higher-flexibility hypothesis. We showed that each Rrp4 subunit within the S. solfataricus RNA-binding ring adopts a distinct conformation and thermal motion distribution pattern. As a result, the previously assumed three-fold symmetric subunit arrangement is broken. Interestingly, it was found that significantly higher conformational flexibility and thermal motions are present in the RNA-binding ring of the crystal structures of the exosome-related PNPases from mesophilic bacteria, Escherichia coli[29] and Streptomyces antibioticus[25]. The RNA-binding ring (occupying 23% of the entire PNPase) in E. coli PNPase is so flexible that it could not be successfully traced from the electron density map [29]. It is therefore likely the RNA-binding ring may become even more dynamic in its native thermophilic environment.



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