5′-end surveillance by Xrn2 acts as a shared mechanism for mammalian pre-rRNA maturation and decay

Wang, Minshi; Pestov, Dimitri G.

doi:10.1093/nar/gkq1050

Cited by 90 publications

(135 citation statements)

References 61 publications

(88 reference statements)

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“…S10D, probe hITS1b) processing intermediates, which are normally eliminated from the cell by the 5 0 -3 0 exoribonucleolytic activity of hXRN2. 11,36 However, in agreement with the primer extension results, hXRN2 silencing did not significantly influence any of the phenotypes associated with hUTP24 mutation.…”

supporting

confidence: 87%

hUTP24 is essential for processing of the human rRNA precursor at site A₁, but not at site A₀

et al. 2015

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Production of ribosomes relies on more than 200 accessory factors to ensure the proper sequence of steps and faultless assembly of ribonucleoprotein machinery. Among trans-acting factors are numerous enzymes, including ribonucleases responsible for processing the large rRNA precursor synthesized by RNA polymerase I that encompasses sequences corresponding to mature 18S, 5.8S, and 25/28S rRNA. In humans, the identity of most enzymes responsible for individual processing steps, including endoribonucleases that cleave pre-rRNA at specific sites within regions flanking and separating mature rRNA, remains largely unknown. Here, we investigated the role of hUTP24 in rRNA maturation in human cells. hUTP24 is a human homolog of the Saccharomyces cerevisiae putative PIN domaincontaining endoribonuclease Utp24 (yUtp24), which was suggested to participate in the U3 snoRNA-dependent processing of yeast pre-rRNA at sites A 0 , A 1 , and A 2 . We demonstrate that hUTP24 interacts to some extent with proteins homologous to the components of the yeast small subunit (SSU) processome. Moreover, mutation in the putative catalytic site of hUTP24 results in slowed growth of cells and reduced metabolic activity. These effects are associated with a defect in biogenesis of the 40S ribosomal subunit, which results from decreased amounts of 18S rRNA as a consequence of inaccurate pre-rRNA processing at the 5 0 -end of the 18S rRNA segment (site A 1 ). Interestingly, and in contrast to yeast, site A 0 located upstream of A 1 is efficiently processed upon UTP24 dysfunction. Finally, hUTP24 inactivation leads to aberrant processing of 18S rRNA 2 nucleotides downstream of the normal A 1 cleavage site.

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supporting

confidence: 87%

hUTP24 is essential for processing of the human rRNA precursor at site A₁, but not at site A₀

et al. 2015

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“…The combined endo-and exonucleolytic activities of Rrp44 (Dis3) are responsible for degradation of the fragment between the A0 site and at the 5 ′ end of the pre-rRNA (Lebreton et al 2008;Schaeffer et al 2009;Schneider et al 2009), while a fragment generated by cleavages at A0 and the 5 ′ end of the mature 18S rRNA accumulates when Rat1 is deleted (Petfalski et al 1998). Similar roles for the mouse homologs of these enzymes have been suggested (Kent et al 2009;Wang and Pestov 2011), but 5 ′ ETS fragment turnover and aberrant pre-rRNA degradation have not been described in human cells.…”

Section: Introductionmentioning

confidence: 69%

“…The major nuclear 5 ′ to 3 ′ exonuclease XRN2 is important for A ′ cleavage in several different organisms (ZakrzewskaPlaczek et al 2010;Wang and Pestov 2011;Sloan et al 2013b) and has also been shown to be important for turnover of the 5 ′ ETS fragment generated by this cleavage in mouse cells (ETS1) (Fig. 3A).…”

Section: Resultsmentioning

confidence: 99%

“…is not yet fully understood (Zakrzewska-Placzek et al 2010;Wang and Pestov 2011;Sloan et al 2013b). We recently observed that reducing the levels of XRN2 affects the balance of alternative ITS1 processing pathways, and we hypothesize that XRN2 may play a more general role in coordinating the optimal order of multiple pre-rRNA cleavages (Sloan et al 2013b).…”

Section: Introductionmentioning

confidence: 99%

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The roles of SSU processome components and surveillance factors in the initial processing of human ribosomal RNA

Sloan

Bohnsack

Schneider

et al. 2014

RNA

102

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During eukaryotic ribosome biogenesis, three of the mature ribosomal (r)RNAs are released from a single precursor transcript (pre-rRNA) by an ordered series of endonucleolytic cleavages and exonucleolytic processing steps. Production of the 18S rRNA requires the removal of the 5 ′ external transcribed spacer (5 ′ ETS) by endonucleolytic cleavages at sites A0 and A1/site 1. In metazoans, an additional cleavage in the 5 ′ ETS, at site A ′ , upstream of A0, has also been reported. Here, we have investigated how A ′ processing is coordinated with assembly of the early preribosomal complex. We find that only the tUTP (UTP-A) complex is critical for A ′ cleavage, while components of the bUTP (UTP-B) and U3 snoRNP are important, but not essential, for efficient processing at this site. All other factors involved in the early stages of 18S rRNA processing that were tested here function downstream from this processing step. Interestingly, we show that the RNA surveillance factors XRN2 and MTR4 are also involved in A ′ cleavage in humans. A ′ cleavage is largely bypassed when XRN2 is depleted, and we also discover that A ′ cleavage is not always the initial processing event in all cell types. Together, our data suggest that A ′ cleavage is not a prerequisite for downstream pre-rRNA processing steps and may, in fact, represent a quality control step for initial pre-rRNA transcripts. Furthermore, we show that components of the RNA surveillance machinery, including the exosome and TRAMP complexes, also play key roles in the recycling of excised spacer fragments and degradation of aberrant pre-rRNAs in human cells.

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“…This process was mainly characterized in yeast and, surprisingly, only recently investigated in human cells, revealing that pre-rRNA processing pathways are notably different in metazoan: ∼27% of human factors have distinct or additional functions in pre-rRNA processing compared with their yeast orthologs, and several pre-RNA processing factors have no yeast homolog (26,29). XRN2 (homolog of yeast XRN2/Rat1) plays a major role in rRNA maturation, coordinating the optimal order of multiple pre-rRNA cleavages (25); it is essential for degradation of 5′-extended 45.5S and 34.5S pre-rRNAs forms, it removes ITS-1-derived extensions to generate 32S from 32.5S pre-rRNA, and it promotes decay of 5′-01, 5′-A0, and E2 fragments, generated by endonucleolytic cleavages in the 5′ETS/ITS1 region in human cells (27)(28)(29) (Fig. 4A).…”

Section: Resultsmentioning

confidence: 99%

Human NF-κB repressing factor acts as a stress-regulated switch for ribosomal RNA processing and nucleolar homeostasis surveillance

Coccia

Rossi

Riccio

et al. 2017

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

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The nucleolus, a dynamic nuclear compartment long regarded as the cell ribosome factory, is emerging as an important player in the regulation of cell survival and recovery from stress. In larger eukaryotes, the stress-induced transcriptional response is mediated by a family of heat-shock transcription factors. Among these, HSF1, considered the master regulator of stress-induced transcriptional responses, controls the expression of cytoprotective heat shock proteins (HSPs), molecular chaperones/cochaperones constituting a major component of the cell protein quality control machinery essential to circumvent stress-induced degradation and aggregation of misfolded proteins. Herein we identify human NF-κB repressing factor (NKRF) as a nucleolar HSP essential for nucleolus homeostasis and cell survival under proteotoxic stress. NKRF acts as a thermosensor translocating from the nucleolus to the nucleoplasm during heat stress; nucleolar pools are replenished during recovery upon HSF1-mediated NKRF resynthesis. Silencing experiments demonstrate that NKRF is an unconventional HSP crucial for correct ribosomal RNA (rRNA) processing and preventing aberrant rRNA precursors and discarded fragment accumulation. These effects are mediated by NKRF interaction with the 5′-to-3′ exoribonuclease XRN2, a key coordinator of multiple pre-rRNA cleavages, driving mature rRNA formation and discarded rRNA decay. Under stress conditions, NKRF directs XRN2 nucleolus/nucleoplasm trafficking, controlling 5′-to-3′ exoribonuclease nucleolar levels and regulating rRNA processing. Our study reveals a different aspect of rRNA biogenesis control in human cells and sheds light on a sophisticated mechanism of nucleolar homeostasis surveillance during stress.heat shock factor 1 | NF-kappaB | nucleolus | proteotoxic stress | rRNA processing

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5′-end surveillance by Xrn2 acts as a shared mechanism for mammalian pre-rRNA maturation and decay

Cited by 90 publications

References 61 publications

hUTP24 is essential for processing of the human rRNA precursor at site A₁, but not at site A₀

hUTP24 is essential for processing of the human rRNA precursor at site A₁, but not at site A₀

The roles of SSU processome components and surveillance factors in the initial processing of human ribosomal RNA

Human NF-κB repressing factor acts as a stress-regulated switch for ribosomal RNA processing and nucleolar homeostasis surveillance

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5′-end surveillance by Xrn2 acts as a shared mechanism for mammalian pre-rRNA maturation and decay

Cited by 90 publications

References 61 publications

hUTP24 is essential for processing of the human rRNA precursor at site A1, but not at site A0

hUTP24 is essential for processing of the human rRNA precursor at site A1, but not at site A0

The roles of SSU processome components and surveillance factors in the initial processing of human ribosomal RNA

Human NF-κB repressing factor acts as a stress-regulated switch for ribosomal RNA processing and nucleolar homeostasis surveillance

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hUTP24 is essential for processing of the human rRNA precursor at site A₁, but not at site A₀

hUTP24 is essential for processing of the human rRNA precursor at site A₁, but not at site A₀