The ribosome assembly factor Nop53 controls association of the RNA exosome with pre-60S particles in yeast

Abstract

Edited by Karin Musier-Forsyth Eukaryotic ribosomal biogenesis is a high-energy-demanding and complex process that requires hundreds of transacting factors to dynamically build the highly-organized 40S and 60S subunits. Each ribonucleoprotein complex comprises specific rRNAs and ribosomal proteins that are organized into functional domains. The RNA exosome complex plays a crucial role as one of the pre-60S-processing factors, because it is the RNase responsible for processing the 7S pre-rRNA to the mature 5.8S rRNA. The yeast pre-60S assembly factor Nop53 has previously been shown to associate with the nucleoplasmic pre-60S in a region containing the "foot" structure assembled around the 3 end of the 7S pre-rRNA. Nop53 interacts with 25S rRNA and with several 60S assembly factors, including the RNA exosome, specifically, with its catalytic subunit Rrp6 and with the exosome-associated RNA helicase Mtr4. Nop53 is therefore considered the adaptor responsible for recruiting the exosome complex for 7S processing. Here, using proteomics-based approaches in budding yeast to analyze the effects of Nop53 on the exosome interactome, we found that the exosome binds pre-ribosomal complexes early during the ribosome maturation pathway. We also identified interactions through which Nop53 modulates exosome activity in the context of 60S maturation and provide evidence that in addition to recruiting the exosome, Nop53 may also be important for positioning the exosome during 7S processing. On the basis of these findings, we propose that the exosome is recruited much earlier during ribosome assembly than previously thought, suggesting the existence of additional interactions that remain to be described.

Nucleolar localization of the yeast RNA exosome subunit Rrp44 hints at early pre-rRNA processing as its main function

“…The results shown here reinforces the importance of the exosome for pre-rRNA processing and quality control, by showing that the exosome is mainly concentrated in the nucleolus. The concentration of the exosome in the nucleolus also corroborate recent data showing the interaction of exosome subunits with pre-ribosomal particles 90S, pre-40S, and pre-60S, interactions that were stabilized by the inhibition of pre-rRNA processing by the depletion of pre-60S factor Nop53 (55).…”

Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae

“…It would also evidence that the RNA Pol I transcription elongation rate and rRNA processing are functionally coupled (Schneider et al 2006(Schneider et al , 2007Scull and Schneider 2019). In any case, our results do not discard a mild impact of exosome activity on 7S rRNA processing given that its Rrp6 subunit, which is needed for 7S rRNA processing (Guglielmi and Werner 2002;Cepeda et al 2019), associates less efficiently with chromatin in the bud27Δ mutant (our unpublished data).…”

Lytic Reactivation of the Kaposi’s sarcoma-associated herpesvirus (KSHV) is Accompanied by Major Nucleolar Alterations

“…6B). Similarly, the nucleolar exosome recruiting and assembly factor, PICT-1 [74,75] also shared redistribution kinetics and pattern with UBF ( Fig. 6C).…”

“…This was associated with extensive redistribution of the nucleolar proteins UBF, Fibrillarin and NPM1 that normally reside at three distinct sub-nucleolar sites. The RNA polymerase I transcription factor UBF, the large RNA polymerase I subunit RPA194, and the vBcl-2 nucleolar partner PICT-1 [57], which also functions in ribosomal biogenesis and in attenuation of the interferon response [75,86], concomitantly redistributed and colocalized in dot-like structures. The RNA methyltransferase Fibrillarin redistributed later, presenting a few large foci surrounded by dense chromatin, and only partially colocalized with UBF.…”