Comparative Multiplexed Mass Spectrometric Analyses of Endogenously Expressed Yeast Nuclear and Cytoplasmic Exosomes

Synowsky, Silvia; Wijk, Martin van; Raijmakers, Reinout; Heck, Albert J. R.

doi:10.1016/j.jmb.2008.11.011

Cited by 55 publications

(53 citation statements)

References 50 publications

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“…Figure 2B shows that Ski6 was mostly concentrated in a complex of molecular mass 600 kDa. We concluded, based on this observation and on the expected size of the nuclear exosome in vivo (21), that the 600 kDa complex contained the entire nuclear exosome. Trf4, a subunit of the TRAMP complex, was also found in the fractions in the 600 kDa range.…”

Section: Fu Affects the Association Of Rrp6 With Multimolecular Compmentioning

confidence: 55%

The Incorporation of 5-Fluorouracil into RNA Affects the Ribonucleolytic Activity of the Exosome Subunit Rrp6

Silverstein

Valdivia²,

Visa³

2011

Molecular Cancer Research

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5-Fluorouracil (5FU) is a fluoropyrimidine used for the treatment of solid tumors. 5FU is a precursor of dTTP and UTP during biogenesis, and it interferes with both DNA and RNA metabolism. The RNA exosome, a multisubunit complex with ribonucleolytic activity, has been identified as one of the targets of 5FU in yeast. Studies in human cells have shown that the catalytic subunit of the nuclear exosome, Rrp6, is specifically targeted. Here, we have investigated the direct effect of 5FU on the activity of Rrp6 in Drosophila S2 cells, and we have identified two aspects of Rrp6 function that are altered by 5FU. First, gel filtration analysis revealed that the repertoire of multimolecular complexes that contain Rrp6 is modified by exposure to 5FU, which is consistent with the proposal that incorporation of 5FU into RNA leads to the sequestration of Rrp6 in ribonucleoprotein complexes. Second, the incorporation of 5FU into RNA renders the RNA less susceptible to degradation by Rrp6, as shown by Rrp6 activity assays in vitro. Our results imply that aberrant transcripts synthesized in 5FU-treated cells cannot be turned over efficiently by the surveillance machinery. Together with previous results on the mechanisms of action of 5FU, our findings suggest that the cytotoxicity of 5FU at the RNA level is the result of at least three different effects: the increased levels of retroviral transcripts with mutagenic potential, the reduced synthesis of ribosomes, and the inhibition of the nuclear RNA surveillance pathways. Drugs that reinforce any of these effects may boost the cytotoxicity of 5FU. Mol Cancer Res; 9(3); 332-40. Ó2011 AACR.

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Section: Fu Affects the Association Of Rrp6 With Multimolecular Compmentioning

confidence: 55%

The Incorporation of 5-Fluorouracil into RNA Affects the Ribonucleolytic Activity of the Exosome Subunit Rrp6

Silverstein

Valdivia²,

Visa³

2011

Molecular Cancer Research

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“…has not been observed as a phosphoprotein in mass spectrometric analyses of exosome complexes 79,80 or in orthophosphate in vivo labeling experiments (our unpublished data).…”

Section: Structure Of Rrp47mentioning

confidence: 84%

Rrp6, Rrp47 and Cofactors of the Nuclear Exosome

Butler

Mitchell

2010

Advances in Experimental Medicine and Biology

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This chapter reviews the present state of knowledge on the activity of enzymes that function with the RNA exosome in the nucleus. In this compartment, the exosome interacts physically and functionally with the exoribonuclease Rrp6 and several cofactors, most prominently Rrp47 and the TRAMP complex. These interactions decide the fate of RNA precursors from transcription through the formation of mature ribonucleoprotein particles (RNPs) and the export of the RNPs to the cytoplasm. The nuclear exosome catalyzes the formation of the mature 3' ends of many of these RNAs, but in other cases degrades the RNAs to mononucleotides. Co-factors such as Mpp6, TRAMP and the Nrd1/Nab3 complex play important roles in determining the outcome of the interaction of RNPs with the nuclear exosome. The details that govern the specificity of these decisions remain a rich source for future investigation.4

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“…Biochemical approaches to purify exosome complexes specifically from the nucleus or cytoplasm have shown that certain exosome subunits (Csl4, Rrp4, Rrp45, Rrp46, and Mtr3) were more prevalent in cytoplasmic complexes, and others (Rrp41, Rrp43, Dis3, and Rrp6) were over-represented in nuclear complexes (Synowsky et al 2009). Only Rrp40 and Rrp42 were approximately evenly distributed between complexes purified from nuclear and cytoplasmic sources (Synowsky et al 2009).…”

Section: Distinct Complexes Are Purified From Yeast and Fly Cellsmentioning

confidence: 99%

The exozyme model: A continuum of functionally distinct complexes

Kiss¹,

Andrulis²

2010

RNA

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Exosome complexes are composed of 10 to 11 subunits and are involved in multiple facets of 39 / 59 RNA processing and turnover. The current paradigm stipulates that a uniform, stoichiometric core exosome, composed of single copies of each subunit, carries out all RNA metabolic functions in vivo. While core composition is well established in vitro, available genetic, cell biological, proteomic, and transcriptomic data raise questions about whether individual subunits contribute to RNA metabolic functions exclusively within the complex. Here, we recount the current understanding of the core exosome model and show predictions of the core model that are not satisfied by the available evidence. To resolve this discrepancy, we propose the exozyme hypothesis, a novel model stipulating that while exosome subunits can and do carry out certain functions within the core, subsets of exosome subunits and cofactors also assemble into a continuum of compositionally distinct complexesexozymes-with different RNA specificities. The exozyme model is consistent with all published data and provides a new framework for understanding the general mechanisms and regulation of RNA processing and turnover.

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Comparative Multiplexed Mass Spectrometric Analyses of Endogenously Expressed Yeast Nuclear and Cytoplasmic Exosomes

Cited by 55 publications

References 50 publications

The Incorporation of 5-Fluorouracil into RNA Affects the Ribonucleolytic Activity of the Exosome Subunit Rrp6

The Incorporation of 5-Fluorouracil into RNA Affects the Ribonucleolytic Activity of the Exosome Subunit Rrp6

Rrp6, Rrp47 and Cofactors of the Nuclear Exosome

The exozyme model: A continuum of functionally distinct complexes

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