Yeast R2TP Interacts with Extended Termini of Client Protein Nop58p

Yu, Ge; Zhao, Yu; Tian, Shaoxiong; Rai, Jay; He, Huan; Spear, John; Sousa, Duncan; Fan, Jinbo; Yu, Hong-Guo; Stagg, Scott M.; Li, Hong

doi:10.1038/s41598-019-56712-4

Cited by 6 publications

(11 citation statements)

References 59 publications

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Section: Resultsmentioning

confidence: 99%

“…We have previously characterized the growth phenotype of Δ pih1 strain 27 . The Δ pih1 strain exhibited slow growth at non-permissive temperatures, similar to that observed in previous studies 20 , 22 , and showed synthetic lethality with C-terminally deleted Nop58, a core 90S assembly factor 27 . Here we performed single particle reconstruction of 90S isolated from the Δ pih1 strain grown to a high optical density (Materials and Methods).…”

Section: Resultsmentioning

confidence: 99%

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Artificial intelligence-assisted cryoEM structure of Bfr2-Lcp5 complex observed in the yeast small subunit processome

et al. 2022

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Eukaryotic ribosome is maturated through an elaborate process that includes modification, processing and folding of pre-ribosomal RNA (pre-rRNAs) by a series of ribosome assembly intermediates. More than 70 factors participate in the dynamic assembly and disassembly of the small subunit processome (90S) inside nucleolus, leading to the early maturation of small subunit. The 5’ domain of the 18S rRNA is the last to be incorporated into the stable 90S prior to the cleavage of pre-rRNA at the A1 site. This step is facilitated by the Kre33-Enp2-Bfr2-Lcp5 protein module with the participation of the DEAD-box protein Dbp4. Though structures of Kre33 and Enp2 have been modeled in previously observed 90S structures, that of Bfr2-Lcp5 complex remains unavailable. Here, we report an AlphaFold-assisted structure determination of the Bfr2-Lcp5 complex captured in a 3.99 Å − 7.24 Å cryoEM structure of 90S isolated from yeast cells depleted of Pih1, a chaperone protein of the 90S core assembly. The structure model is consistent with the protein-protein interaction results and the secondary structures of recombinant Bfr2 and Bfr2-Lcp5 complex obtained by Circular Dichroism. The Bfr2-Lcp5 complex interaction mimics that of exosome factors Rrp6-Rrp47 and acts to regulate 90S transitions.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Artificial intelligence-assisted cryoEM structure of Bfr2-Lcp5 complex observed in the yeast small subunit processome

et al. 2022

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“…Similarly, the Nop56 and Nop58 proteins have acquired a number of additional binding partners in eukaryotes with respect to archaea. While some of these interactions have been found to engage the carboxy-terminal domain (such as the AAA+ ATPase R2TP complex recruiting the carboxy-terminal unstructured tail of Nop58 [ Yu et al 2019 ]), the binding mode of many other partners is unknown, as for example that of the Drosophila protein hoip, which binds both Nop56 and Nop58 ( Murata et al 2008 ), or of the component of the R2TP complex Nop17, which binds Nop58 during the assembly of the Box C/D snoRNP ( Prieto et al 2015 ). In addition, Nop56 has been suggested to act in Burkitt's lymphoma associated with c-Myc mutations ( Cowling et al 2014 ) through a yet-uncharacterized mechanism.…”

Section: Discussionmentioning

confidence: 99%

High-resolution structure of eukaryotic Fibrillarin interacting with Nop56 amino-terminal domain

Höfler

Lukat

Blankenfeldt

et al. 2021

RNA

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Ribosomal RNA (rRNA) carries extensive 2′-O-methyl marks at functionally important sites. This simple chemical modification is thought to confer stability, promote RNA folding, and contribute to generate a heterogenous ribosome population with a yet-uncharacterized function. 2′-O-methylation occurs both in archaea and eukaryotes and is accomplished by the Box C/D RNP enzyme in an RNA-guided manner. Extensive and partially conflicting structural information exists for the archaeal enzyme, while no structural data is available for the eukaryotic enzyme. The yeast Box C/D RNP consists of a guide RNA, the RNA-primary binding protein Snu13, the two scaffold proteins Nop56 and Nop58, and the enzymatic module Nop1. Here we present the high-resolution structure of the eukaryotic Box C/D methyltransferase Nop1 from Saccharomyces cerevisiae bound to the amino-terminal domain of Nop56. We discuss similarities and differences between the interaction modes of the two proteins in archaea and eukaryotes and demonstrate that eukaryotic Nop56 recruits the methyltransferase to the Box C/D RNP through a protein–protein interface that differs substantially from the archaeal orthologs. This study represents a first achievement in understanding the evolution of the structure and function of these proteins from archaea to eukaryotes.

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“…This echoes the lack of SMN complex in S. cerevisiae and suggests that biogenesis of sn/snoRNPs may follow simplified pathways in budding yeast. In this organism, Nop58p recruitment on R2TP has been proposed to be mediated by Pih1p, which may have evolved to compensate the absence of NOPCHAP1 ( 28 , 64 ).…”

Section: Discussionmentioning

confidence: 99%

NOPCHAP1 is a PAQosome cofactor that helps loading NOP58 on RUVBL1/2 during box C/D snoRNP biogenesis

Abel

Paiva

Bizarro

et al. 2020

Nucleic Acids Research

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The PAQosome is a large complex composed of the HSP90/R2TP chaperone and a prefoldin-like module. It promotes the biogenesis of cellular machineries but it is unclear how it discriminates closely related client proteins. Among the main PAQosome clients are C/D snoRNPs and in particular their core protein NOP58. Using NOP58 mutants and proteomic experiments, we identify different assembly intermediates and show that C12ORF45, which we rename NOPCHAP1, acts as a bridge between NOP58 and PAQosome. NOPCHAP1 makes direct physical interactions with the CC-NOP domain of NOP58 and domain II of RUVBL1/2 AAA+ ATPases. Interestingly, NOPCHAP1 interaction with RUVBL1/2 is disrupted upon ATP binding. Moreover, while it robustly binds both yeast and human NOP58, it makes little interactions with NOP56 and PRPF31, two other closely related CC-NOP proteins. Expression of NOP58, but not NOP56 or PRPF31, is decreased in NOPCHAP1 KO cells. We propose that NOPCHAP1 is a client-loading PAQosome cofactor that selects NOP58 to promote box C/D snoRNP assembly.

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Yeast R2TP Interacts with Extended Termini of Client Protein Nop58p

Cited by 6 publications

References 59 publications

Artificial intelligence-assisted cryoEM structure of Bfr2-Lcp5 complex observed in the yeast small subunit processome

Artificial intelligence-assisted cryoEM structure of Bfr2-Lcp5 complex observed in the yeast small subunit processome

High-resolution structure of eukaryotic Fibrillarin interacting with Nop56 amino-terminal domain

NOPCHAP1 is a PAQosome cofactor that helps loading NOP58 on RUVBL1/2 during box C/D snoRNP biogenesis

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