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

Okuda, Ellen Kazumi; Gonzales-Zubiate, Fernando A.; Gadal, Olivier; Oliveira, Carla C.

doi:10.1074/jbc.ra120.013589

Cited by 6 publications

(5 citation statements)

References 71 publications

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“…5) but were more abundant in the rrp6Δ strain, suggesting that their levels are dependent on Rrp6 protein but not its exoribonuclease activity. While localization of exosomes might differ in the absence of Rrp6 protein, a recent study showed that depletion of Rrp6 did not alter nuclear transport or subcellular localization of Dis3 or other core exosome subunits (54). These results are also consistent with prior studies in which a catalytically inactive Rrp6 reduced the accumulation of poly(A) + RNAs when expressed in rrp6Δ yeast strains (55).…”

Section: Biochemistrysupporting

confidence: 87%

Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome

Das

Zattas

Zinder

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Quality control requires discrimination between functional and aberrant species to selectively target aberrant substrates for destruction. Nuclear RNA quality control in Saccharomyces cerevisiae includes the TRAMP complex that marks RNA for decay via polyadenylation followed by helicase-dependent 3′ to 5′ degradation by the RNA exosome. Using reconstitution biochemistry, we show that polyadenylation and helicase activities of TRAMP cooperate with processive and distributive exoribonuclease activities of the nuclear RNA exosome to protect stable RNA from degradation while selectively targeting and degrading less stable RNA. Substrate discrimination is lost when the distributive exoribonuclease activity of Rrp6 is inactivated, leading to degradation of stable and unstable RNA species. These data support a proofreading mechanism in which deadenylation by Rrp6 competes with Mtr4-dependent degradation to protect stable RNA while selectively targeting and degrading unstable RNA.

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Section: Biochemistrysupporting

confidence: 87%

Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome

Das

Zattas

Zinder

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…The depletion of Srp1 or Kap95 levels in the cell leads to Rrp44 partial mislocalization, evidenced by a strong signal in the cytoplasm. Unlike Rrp6, the depletion of Sxm1 did not show any effect on Rrp44 localization 30 .…”

Section: Depletion Of Karyopherins Affect the Localization Of Exosome Subunitsmentioning

confidence: 68%

Mechanisms of Nuclear Transport in the cell: RNA exosome in Saccharomyces cerevisiae

Rech

Gonzales-Zubiate

2020

Self Cite

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Ribonucleases (RNases) functions in the cell include precise maturation of non- coding RNAs and degradation of specific RNA transcripts that are no longer necessary. RNAses are present in the cell as single units or assembled as multimeric complexes; one of these complexes is the RNA exosome, a highly conserved complex essential for RNA processing and degradation. In the yeast Saccharomyces cerevisiae, the RNA exosome comprises eleven subunits, two with catalytic activity: Rrp6 and Rrp44, where the Rrp6 subunit is exclusively nuclear. Despite the RNA exosome has been intensively investigated since its discovery in 1997, only a few studies were accomplished concerning its nuclear transport. This review describes recent research about cellular localization and transport of this essential complex.

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“…RNA exosomes play a pivotal role in processing and maturing rRNAs by trimming pre-rRNA intermediates and eliminating rRNA by-products [102][103][104]. In Arabidopsis, the loss of components of nuclear RNA exosome and cytoplasmic RNA decay processes triggers the production of aberrant rRNA-derived small RNAs [101,102].…”

Section: Aberrant Rrnas Serve As Sources Of Antisense Small Rnas That...mentioning

confidence: 99%

Functions of RNAi Pathways in Ribosomal RNA Regulation

Shatskikh,

Fefelova,

Klenov

2024

ncRNA

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Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation. Data from diverse eukaryotic organisms suggest the potential involvement of small RNAs in various molecular processes related to the rDNA transcription and rRNA fate. Endogenous siRNAs are integral to the chromatin-based silencing of rDNA loci in plants and have been shown to repress rDNA transcription in animals. Small RNAs also play a role in maintaining the integrity of rDNA clusters and may function in the cellular response to rDNA damage. Studies on the impact of RNAi and small RNAs on rRNA provide vast opportunities for future exploration.

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

Cited by 6 publications

References 71 publications

Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome

Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome

Mechanisms of Nuclear Transport in the cell: RNA exosome in Saccharomyces cerevisiae

Functions of RNAi Pathways in Ribosomal RNA Regulation

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