The archaeal exosome core is a hexameric ring structure with three catalytic subunits

Lorentzen, Esben; Walter, Pamela; Fribourg, Sébastien; Evguenieva‐Hackenberg, Elena; Klug, Gabriele; Conti, Elena

doi:10.1038/nsmb952

Cited by 196 publications

(252 citation statements)

References 34 publications

Supporting

Mentioning

231

Contrasting

Unclassified

Order By: Relevance

“…However, several hyperthermophilic and methanogenic Archaea contain a protein complex that is composed of two proteins (Rrp41 and Rrp42) homologous to RNase PH and one protein containing a KH/S1 domain [33]. Three copies of the three proteins form a nine-subunit complex termed the archaeal exosome that, as with PNPase, is responsible for the polyadenylation and degradation of RNA [29,30,[34][35][36][37]. Moreover, crystallographic analysis of archaeal exosome has revealed a structure very similar to the PNPase of bacteria (Figure 3).…”

Section: Similar Structure Of the Rnase Ph Pnpase And Exosome Complexesmentioning

confidence: 99%

“…Similarities in the structure of the RNase PH and 3¢ fi 5¢ RNA degradation machines: the PNPase and the exosome. The structure of the RNase PH [22,23], the bacterial PNPase [27], archaeal [29,30] and eukaryotic [31] exosomes, as well as the predicted structure of the chloroplast PNPase [24], are shown in order to compare the ring shape of these complexes. The molecular surfaces of these structures are represented in the same view and colored as in Figure 2.…”

Section: Chloroplastmentioning

confidence: 99%

“…The structures were generated using Pymol (see The PyMOL Molecular Graphics System in Further Information). Rrp41 [29,30] Rrp44 [31,49] Rrp6 and Rrp44 [31] hRrp41/Rrp45…”

Section: Chloroplastmentioning

confidence: 99%

See 2 more Smart Citations

The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines

2007

View full text Add to dashboard Cite

The structure and function of polynucleotide phosphorylase (PNPase) and the exosome, as well as their associated RNA-helicases proteins, are described in the light of recent studies. The picture raised is of an evolutionarily conserved RNA-degradation machine which exonucleolytically degrades RNA from 3¢ to 5¢. In prokaryotes and in eukaryotic organelles, a trimeric complex of PNPase forms a circular doughnutshaped structure, in which the phosphorolysis catalytic sites are buried inside the barrel-shaped complex, while the RNA binding domains create a pore where RNA enters, reminiscent of the protein degrading complex, the proteasome. In some archaea and in the eukaryotes, several different proteins form a similar circle-shaped complex, the exosome, that is responsible for 3¢ to 5¢ exonucleolytic degradation of RNA as part of the processing, quality control, and general RNA degradation process. Both PNPase in prokaryotes and the exosome in eukaryotes are found in association with protein complexes that notably include RNA helicase.

show abstract

Section: Similar Structure Of the Rnase Ph Pnpase And Exosome Complexesmentioning

confidence: 99%

Section: Chloroplastmentioning

confidence: 99%

See 1 more Smart Citation

The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines

2007

View full text Add to dashboard Cite

show abstract

“…In the trimer, the RPDs are arranged in a catalytically active hexameric ring, on the top of which the KH and S1 domains are located [4]. In the archaeal exosome, the catalytically active hexameric ring is composed of alternating, RPD-domain containing Rrp41 and Rrp42 polypeptides [5]. On the top of the hexamer, a trimeric cap of RNA-binding subunits is located, which may contain Rrp4 (with an S1 domain and a KH domain), Csl4 (with an S1 domain and Zn-ribbon domain) (Fig.…”

Section: Introductionmentioning

confidence: 99%

The evolutionarily conserved subunits Rrp4 and Csl4 confer different substrate specificities to the archaeal exosome

Roppelt

Klug

Evguenieva‐Hackenberg

2010

FEBS Letters

Self Cite

View full text Add to dashboard Cite

a b s t r a c tWe studied the substrate specificity of the exosome of Sulfolobus solfataricus using the catalytically active Rrp41-Rrp42-hexamer and complexes containing the RNA-binding subunits Rrp4 or Csl4. The conservation of both Rrp4 and Csl4 in archaeal and eukaryotic exosomes suggests specific functions for each of them. We found that they confer different specificities to the exosome: RNA with an Apoor 3 0 -end is degraded with higher efficiency by the Csl4-exosome, while the Rrp4-exosome strongly prefers poly(A)-RNA. High C-content and polyuridylation negatively influence RNA processing by all complexes, and, in contrast to the hexamer, the Rrp4-exosome prefers longer substrates.

show abstract

“…The core of the exosome has a barrel-like architecture (reviewed by Lorentzen et al, 2008). The barrel is made of nine protein subunits organized into two rings, a hexameric ring and a trimeric ring, and the structure of the barrel is conserved throughout evolution (Lorentzen et al, 2005;Liu et al, 2006;Wang et al, 2007). Two additional proteins, Dis3/Rrp44 and Rrp6, are associated with the barrel and provide the ribonucleolytic activity (Liu et al, 2006;Dziembowski et al, 2007;Schneider et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

The Exosome Associates Cotranscriptionally with the Nascent Pre-mRNP through Interactions with Heterogeneous Nuclear Ribonucleoproteins

Hessle¹,

Björk²,

Sokolowski³

et al. 2009

MBoC

View full text Add to dashboard Cite

Eukaryotic cells have evolved quality control mechanisms to degrade aberrant mRNA molecules and prevent the synthesis of defective proteins that could be deleterious for the cell. The exosome, a protein complex with ribonuclease activity, is a key player in quality control. An early quality checkpoint takes place cotranscriptionally but little is known about the molecular mechanisms by which the exosome is recruited to the transcribed genes. Here we study the core exosome subunit Rrp4 in two insect model systems, Chironomus and Drosophila. We show that a significant fraction of Rrp4 is associated with the nascent pre-mRNPs and that a specific mRNA-binding protein, Hrp59/hnRNP M, interacts in vivo with multiple exosome subunits. Depletion of Hrp59 by RNA interference reduces the levels of Rrp4 at transcription sites, which suggests that Hrp59 is needed for the exosome to stably interact with nascent pre-mRNPs. Our results lead to a revised mechanistic model for cotranscriptional quality control in which the exosome is constantly recruited to newly synthesized RNAs through direct interactions with specific hnRNP proteins. INTRODUCTIONExpression of protein-coding genes is a complex multistep process. Precursor messenger RNAs (pre-mRNAs) are synthesized by RNA polymerase II (Pol-II) and assembled into ribonucleoprotein (RNP) complexes during transcription. The pre-mRNPs must be processed to become mature mRNPs, which are exported to the cytoplasm and translated into protein. Mutations in the DNA or errors in the transcription and processing reactions can lead to the synthesis of aberrant mRNPs. Eukaryotic cells have evolved quality control mechanisms that identify aberrant mRNPs and prevent their expression into protein. In the yeast Saccharomyces cerevisiae there are at least three nuclear steps of mRNP biogenesis that are under surveillance: the cleavage and polyadenylation of the 3Ј end (Hilleren et al., 2001), the assembly of the mRNA-protein complexes (Zenklusen et al., 2002;Luna et al., 2005), and the removal of introns (Galy et al., 2004). In all cases, mRNPs with assembly and/or processing defects are detected by nuclear surveillance mechanisms, retained in the nucleus, and degraded (reviewed by Vinciguerra and Stutz, 2004;Sommer and Nehrbass, 2005;Saguez et al., 2005). Genetic studies in S. cerevisiae have identified the nuclear exosome as a key player in the recognition and retention of defective transcripts (reviewed by Jensen et al., 2003;Houseley et al., 2006;Vanacova and Stefl, 2007;Schmid and Jensen, 2008).The exosome is a protein complex with ribonuclease activity (Mitchell et al., 1997;Allmang et al., 1999;Mitchell and Tollervey, 2000). The core of the exosome has a barrel-like architecture (reviewed by Lorentzen et al., 2008). The barrel is made of nine protein subunits organized into two rings, a hexameric ring and a trimeric ring, and the structure of the barrel is conserved throughout evolution (Lorentzen et al., 2005;Liu et al., 2006;Wang et al., 2007). Two additional proteins, Dis3/Rrp44 and R...

show abstract

The archaeal exosome core is a hexameric ring structure with three catalytic subunits

Cited by 196 publications

References 34 publications

The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines

The PNPase, exosome and RNA helicases as the building components of evolutionarily-conserved RNA degradation machines

The evolutionarily conserved subunits Rrp4 and Csl4 confer different substrate specificities to the archaeal exosome

The Exosome Associates Cotranscriptionally with the Nascent Pre-mRNP through Interactions with Heterogeneous Nuclear Ribonucleoproteins

Contact Info

Product

Resources

About