Structural and functional analysis of the U3 snoRNA binding protein Rrp9

Zhang, Liman; Lin, Jinzhong; Ye, Keqiong

doi:10.1261/rna.037580.112

Cited by 26 publications

(24 citation statements)

References 60 publications

(87 reference statements)

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“…For this, immobilized U3-55k protein (or TIF-IA as a negative control) was incubated with radiolabelled wild-type or mutant U3 RNA, in the absence or presence of increasing amounts of GST-15.5k protein, and bound RNA was visualized by gel electrophoresis and PhosphorImaging. In accord with previous reports 34 35 , this assay revealed that binding of U3-55k to U3 snoRNA is markedly stimulated by the 15.5k protein ( Fig. 4h and Supplementary Fig.…”

Section: Resultssupporting

confidence: 92%

“…It was proposed that binding of 15.5k to the B/C motif is essential for recruitment of U3-55k and for the subsequent nucleation of the SSU processome. However, it remained controversial whether U3-55k interacts with U3 RNA independent of the 15.5k protein 34 35 . To address this issue, we performed northwestern analyses, incubating membrane-bound U3-55k with radioactive-labelled U3 BC RNA.…”

Section: Resultsmentioning

confidence: 99%

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SIRT7-dependent deacetylation of the U3-55k protein controls pre-rRNA processing

et al. 2016

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SIRT7 is an NAD+-dependent protein deacetylase with important roles in ribosome biogenesis and cell proliferation. Previous studies have established that SIRT7 is associated with RNA polymerase I, interacts with pre-ribosomal RNA (rRNA) and promotes rRNA synthesis. Here we show that SIRT7 is also associated with small nucleolar RNP (snoRNPs) that are involved in pre-rRNA processing and rRNA maturation. Knockdown of SIRT7 impairs U3 snoRNA dependent early cleavage steps that are necessary for generation of 18S rRNA. Mechanistically, SIRT7 deacetylates U3-55k, a core component of the U3 snoRNP complex, and reversible acetylation of U3-55k modulates the association of U3-55k with U3 snoRNA. Deacetylation by SIRT7 enhances U3-55k binding to U3 snoRNA, which is a prerequisite for pre-rRNA processing. Under stress conditions, SIRT7 is released from nucleoli, leading to hyperacetylation of U3-55k and attenuation of pre-rRNA processing. The results reveal a multifaceted role of SIRT7 in ribosome biogenesis, regulating both transcription and processing of rRNA.

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Section: Resultssupporting

confidence: 92%

Section: Resultsmentioning

confidence: 99%

SIRT7-dependent deacetylation of the U3-55k protein controls pre-rRNA processing

et al. 2016

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“…The inspection of the sequence of the U3-type snoRNAs resulted in the identification of typical elements of a C/D box snoRNA and of a predicted structure comparable to U3 from yeast ( Figure 3 a [ 69 ]). U3 encoded by chromosome 1 (U3.1) is the plant U3 snoRNA of which the predicted structure is most comparable to the one proposed for yeast U3 ( Figure 3 a).…”

Section: Resultsmentioning

confidence: 99%

The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited

Streit

Shanmugam

Garbelyanski

et al. 2020

Plants

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Ribosome biogenesis is one cell function-defining process. It depends on efficient transcription of rDNAs in the nucleolus as well as on the cytosolic synthesis of ribosomal proteins. For newly transcribed rRNA modification and ribosomal protein assembly, so-called small nucleolar RNAs (snoRNAs) and ribosome biogenesis factors (RBFs) are required. For both, an inventory was established for model systems like yeast and humans. For plants, many assignments are based on predictions. Here, RNA deep sequencing after nuclei enrichment was combined with single molecule species detection by northern blot and in vivo fluorescence in situ hybridization (FISH)-based localization studies. In addition, the occurrence and abundance of selected snoRNAs in different tissues were determined. These approaches confirm the presence of most of the database-deposited snoRNAs in cell cultures, but some of them are localized in the cytosol rather than in the nucleus. Further, for the explored snoRNA examples, differences in their abundance in different tissues were observed, suggesting a tissue-specific function of some snoRNAs. Thus, based on prediction and experimental confirmation, many plant snoRNAs can be proposed, while it cannot be excluded that some of the proposed snoRNAs perform alternative functions than are involved in rRNA modification.

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“…Maturation of 18S rRNA was inhibited, with accumulation of 23S and 27SA2 pre-rRNA ( Figure 4E ). This phenotype reflects inhibition of pre-rRNA cleavage at sites A 0 , A 1 and A 2 , and is characteristic of the effects of loss of U3 or U3-associated proteins, including Rrp9 ( Venema et al , 2000 ; Zhang et al , 2013 ). Rrp9 was shown to interact with U3 in the helix 2 and 4 regions, and box C was shown to be important for Rrp9 binding.…”

Section: Resultsmentioning

confidence: 99%

Mapping targets for small nucleolar RNAs in yeast

Dudnakova¹,

Dunn-Davies²,

Peters³

et al. 2018

Wellcome Open Res

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Background: Recent analyses implicate changes in the expression of the box C/D class of small nucleolar RNAs (snoRNAs) in several human diseases. Methods: Here we report the identification of potential novel RNA targets for box C/D snoRNAs in budding yeast, using the approach of UV crosslinking and sequencing of hybrids (CLASH) with the snoRNP proteins Nop1, Nop56 and Nop58. We also developed a bioinformatics approach to filter snoRNA-target interactions for bona fide methylation guide interactions. Results: We recovered 241,420 hybrids, out of which 190,597 were classed as reproducible, high energy hybrids. As expected, the majority of snoRNA interactions were with the ribosomal RNAs (rRNAs). Following filtering, 117,047 reproducible hybrids included 51 of the 55 reported rRNA methylation sites. The majority of interactions at methylation sites were predicted to guide methylation. However, competing, potentially regulatory, binding was also identified. In marked contrast, following CLASH performed with the RNA helicase Mtr4 only 7% of snoRNA-rRNA interactions recovered were predicted to guide methylation. We propose that Mtr4 functions in dissociating inappropriate snoRNA-target interactions. Numerous snoRNA-snoRNA interactions were recovered, indicating potential cross regulation. The snoRNAs snR4 and snR45 were recently implicated in site-directed rRNA acetylation, and hybrids were identified adjacent to the acetylation sites. We also identified 1,368 reproducible snoRNA-mRNA interactions, representing 448 sites of interaction involving 39 snoRNAs and 382 mRNAs. Depletion of the snoRNAs U3, U14 or snR4 each altered the levels of numerous mRNAs. Targets identified by CLASH were over-represented among these species, but causality has yet to be established. Conclusions: Systematic mapping of snoRNA-target binding provides a catalogue of high-confidence binding sites and indicates numerous potential regulatory interactions.

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Structural and functional analysis of the U3 snoRNA binding protein Rrp9

Cited by 26 publications

References 60 publications

SIRT7-dependent deacetylation of the U3-55k protein controls pre-rRNA processing

SIRT7-dependent deacetylation of the U3-55k protein controls pre-rRNA processing

The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited

Mapping targets for small nucleolar RNAs in yeast

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