Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit

Greber, B.J.; Boehringer, Daniel; Montellese, Christian; Ban, Nenad

doi:10.1038/nsmb.2425

Cited by 98 publications

(134 citation statements)

References 58 publications

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“…Its ortholog in yeast, Arx1, was identified to be a nuclear export receptor for the 60S ribosomal subunit (Hung et al 2008). Structural data in yeast show that Arx1 interacts with the 28S rRNA expansion segment ES27L (Greber et al 2012). It binds the ribosome close to the peptide exit tunnel, where it inhibits the association of translation factors before the maturation of the ribosome is complete.…”

Section: Determination Of the Rrna Interactomes Of Hela Cells By Specmentioning

confidence: 99%

Specific RNP capture with antisense LNA/DNA mixmers

Rogell

Fischer

Rettel

et al. 2017

RNA

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RNA-binding proteins (RBPs) play essential roles in RNA biology, responding to cellular and environmental stimuli to regulate gene expression. Important advances have helped to determine the (near) complete repertoires of cellular RBPs. However, identification of RBPs associated with specific transcripts remains a challenge. Here, we describe "specific ribonucleoprotein (RNP) capture," a versatile method for the determination of the proteins bound to specific transcripts in vitro and in cellular systems. Specific RNP capture uses UV irradiation to covalently stabilize protein-RNA interactions taking place at "zero distance." Proteins bound to the target RNA are captured by hybridization with antisense locked nucleic acid (LNA)/DNA oligonucleotides covalently coupled to a magnetic resin. After stringent washing, interacting proteins are identified by quantitative mass spectrometry. Applied to in vitro extracts, specific RNP capture identifies the RBPs bound to a reporter mRNA containing the Sex-lethal (Sxl) binding motifs, revealing that the Sxl homolog sister of Sex lethal (Ssx) displays similar binding preferences. This method also revealed the repertoire of RBPs binding to 18S or 28S rRNAs in HeLa cells, including previously unknown rRNA-binding proteins.

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Section: Determination Of the Rrna Interactomes Of Hela Cells By Specmentioning

confidence: 99%

Specific RNP capture with antisense LNA/DNA mixmers

Rogell

Fischer

Rettel

et al. 2017

RNA

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“…Their reduction in preribosomes is likely because these structural neighborhoods are not properly assembled when middle-acting RPLs are depleted (see ''Assembly of 60S Ribosomal Subunit Domains Is Hierarchical,'' below). Arx1 binds to RPLs and rRNA sequences around the exit tunnel (Bradatsch et al 2012;Greber et al 2012). Thus, its reduction may reflect proximal effects of RPL assembly on binding of factors; assembly of the exit tunnel might be required to establish proper contacts with Arx1.…”

Section: Binding Of Rpls Is Coupled With Association Of Afs With Prermentioning

confidence: 99%

“…While the binding sites for only a handful of yeast AFs in nascent ribosomes have been identified (Ulbrich et al 2009;Granneman et al 2010Granneman et al , 2011Sengupta et al 2010;Strunk et al 2011;Bradatsch et al 2012;Greber et al 2012;Matsuo et al 2013), recently solved crystal structures of mature yeast ribosomes show in exquisite detail where each individual RP interacts with rRNA (BenShem et al 2011). Knowing these final endpoints of RP localization provides a strategic platform to investigate the connection between spatial and temporal aspects of ribosome biogenesis.…”

mentioning

confidence: 99%

A hierarchical model for assembly of eukaryotic 60S ribosomal subunit domains

et al. 2014

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Despite having high-resolution structures for eukaryotic large ribosomal subunits, it remained unclear how these ribonucleoprotein complexes are constructed in living cells. Nevertheless, knowing where ribosomal proteins interact with ribosomal RNA (rRNA) provides a strategic platform to investigate the connection between spatial and temporal aspects of 60S subunit biogenesis. We previously found that the function of individual yeast large subunit ribosomal proteins (RPLs) in precursor rRNA (pre-rRNA) processing correlates with their location in the structure of mature 60S subunits. This observation suggested that there is an order by which 60S subunits are formed. To test this model, we used proteomic approaches to assay changes in the levels of ribosomal proteins and assembly factors in preribosomes when RPLs functioning in early, middle, and late steps of pre-60S assembly are depleted. Our results demonstrate that structural domains of eukaryotic 60S ribosomal subunits are formed in a hierarchical fashion. Assembly begins at the convex solvent side, followed by the polypeptide exit tunnel, the intersubunit side, and finally the central protuberance. This model provides an initial paradigm for the sequential assembly of eukaryotic 60S subunits. Our results reveal striking differences and similarities between assembly of bacterial and eukaryotic large ribosomal subunits, providing insights into how these RNA-protein particles evolved.

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“…A small number of assembly factors join these midstage intermediates, to catalyze release of the early factors, enable processing of the ITS2 spacer from 27SB pre-rRNA, or facilitate nuclear export of the pre-rRNPs (Saveanu et al 2001;Nissan et al 2002;Lebreton et al 2006a;Kressler et al 2008;Ulbrich et al 2009). Following export, 10-12 late-acting factors dock with cytoplasmic preribosomes, to facilitate the final steps in pre-rRNA processing, assembly of several late r-proteins, and removal of the last 6-8 other assembly factors (Lo et al 2010;Bradatsch et al 2012;Greber et al 2012).…”

Section: Hierarchy Of Assembly: Maturation From Complex To Simpler Prmentioning

confidence: 99%

Ribosome Biogenesis in the YeastSaccharomyces cerevisiae

2013

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Ribosomes are highly conserved ribonucleoprotein nanomachines that translate information in the genome to create the proteome in all cells. In yeast these complex particles contain four RNAs (.5400 nucleotides) and 79 different proteins. During the past 25 years, studies in yeast have led the way to understanding how these molecules are assembled into ribosomes in vivo. Assembly begins with transcription of ribosomal RNA in the nucleolus, where the RNA then undergoes complex pathways of folding, coupled with nucleotide modification, removal of spacer sequences, and binding to ribosomal proteins. More than 200 assembly factors and 76 small nucleolar RNAs transiently associate with assembling ribosomes, to enable their accurate and efficient construction. Following export of preribosomes from the nucleus to the cytoplasm, they undergo final stages of maturation before entering the pool of functioning ribosomes. Elaborate mechanisms exist to monitor the formation of correct structural and functional neighborhoods within ribosomes and to destroy preribosomes that fail to assemble properly. Studies of yeast ribosome biogenesis provide useful models for ribosomopathies, diseases in humans that result from failure to properly assemble ribosomes. TABLE OF CONTENTS Abstract 643Introduction 644

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Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit

Cited by 98 publications

References 58 publications

Specific RNP capture with antisense LNA/DNA mixmers

Specific RNP capture with antisense LNA/DNA mixmers

A hierarchical model for assembly of eukaryotic 60S ribosomal subunit domains

Ribosome Biogenesis in the YeastSaccharomyces cerevisiae

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