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Ribosome assembly coming into focus

Abstract

In the past 25 years, genetic and biochemical analyses of ribosome assembly in yeast have identified most of the factors that participate in this complex pathway and have generated models for the mechanisms driving the assembly. More recently, the publication of numerous cryo-electron microscopy structures of yeast ribosome assembly intermediates has provided near-atomic resolution snapshots of ribosome precursor particles. Satisfyingly, these structural data support the genetic and biochemical models and provide additional mechanistic insight into ribosome assembly. In this Review, we discuss the mechanisms of assembly of the yeast small ribosomal subunit and large ribosomal subunit in the nucleolus, nucleus and cytoplasm. Particular emphasis is placed on concepts such as the mechanisms of RNA compaction, the functions of molecular switches and molecular mimicry, the irreversibility of assembly checkpoints and the roles of structural and functional proofreading of pre-ribosomal particles.

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Fig. 1: Pre-rRNA processing in yeast.
Fig. 2: Assembly of the small ribosomal subunit.
Fig. 3: Cryo-electron microscopy structure of a nucleolar small-subunit precursor.
Fig. 4: Assembly of the large ribosomal subunit.
Fig. 5: Cryo-electron microscopy structures of large-subunit precursors.
Fig. 6: Structural changes occurring in nucleolar and nuclear ribosomal precursors.

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Acknowledgements

The authors thank members of the Woolford laboratory for comments on the manuscript and members of the Klinge laboratory for help with Fig. 2. The authors apologize to those whose work could not be discussed owing to space limitations.

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Nature Reviews Molecular Cell Biology thanks A. Johnson and D. Lafontaine for their contribution to the peer review of this work.

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Glossary

Ribosomal proteins

Seventy-nine protein components of mature ribosomal subunits in yeast. Most are essential for assembly of their respective subunits.

Decoding site

The functional centre of the small subunit, where the anticodon of an amino-acyl tRNA undergoes base pairing with the respective codon in the mRNA.

Peptidyl transferase centre

(PTC). The active site of the large subunit, located in its interface, where ribosomal RNA catalyses the formation of peptide bonds and the hydrolysis of peptidyl-tRNA bonds.

Central pseudoknot

An architectural motif within the small ribosomal subunit ribosomal RNA, at the interface of the four subdomains of the small ribosomal subunit.

Central protuberance

A module that includes the 5S ribonucleoprotein and helices 80 and 82–88 of 25S ribosomal RNA, located at the top of the mature large ribosomal subunit.

GTPase activating centre

(GAC). Within mature, large ribosomal subunits, the site that binds to and activates GTPases that participate in translation initiation and elongation.

P0 stalk

A complex of three ribosomal proteins bound to helices 43 and 44 in 25S ribosomal RNA, which forms a stalk structure in mature large ribosomal subunits, to which translation factors bind.

Polypeptide exit tunnel

(PET). A tunnel through which nascent polypeptides traverse the large ribosomal subunit. It comprises mostly ribosomal RNA and extends from the peptidyl transferase centre to the solvent side of the large subunit.

Small nucleolar ribonucleoproteins

(snoRNPs). Complexes of small nucleolar RNAs (snoRNAs) and proteins. Base pairing of specific snoRNAs with target sequences in ribosomal RNA (rRNA) directs either methylation or pseudouridylation of the rRNA.

Assembly factors

Proteins or protein complexes with roles in ribosome assembly. Most are present in ribosome assembly intermediates but none are components of mature ribosomes.

Molecular mimicry

Refers to the activity of proteins for which the structure mimics that of other proteins (or of RNA). In ribosome assembly, molecular mimicry is used to block distinct sites by steric hindrance and prevent early binding of a structurally related protein.

Molecular switches

Refers to factors that can switch between two states (for example, an assembly factor present or absent in a pre-ribosome) in response to internal hardwiring or an external cue.

External and internal transcribed spacers

RNA sequences in the primary ribosomal RNA (rRNA) transcript, which are removed during ribosome biogenesis by a series of endonucleolytic or exonucleolytic reactions. They are thought to aid in proper folding of nascent rRNA.

90S particles

The very early pre-ribosomal particles containing the 35S pre-ribosomal RNA, which includes transcripts for both small and large ribosomal subunits.

Miller spreads

Visualization of actively transcribed chromatin by electron microscopy of fixed, gently lysed nuclei, first used to look at transcription of ribosomal DNA repeats in Xenopus laevis.

AAA-ATPases

(ATPases associated with diverse cellular activities). There are three different AAA-ATPases that function as ribosome assembly factors to remove other assembly factors from pre-ribosomes.

Aptamers

RNA oligonucleotides that are able to adopt a distinct shape and bind to a specific target with high specificity and affinity.

Multimodal binding

Binding of a single protein to multiple ligands through separate binding sites in the protein.

Exosome

A protein complex with 3ʹ to 5ʹ exonuclease activity, which processes cleaved pre-ribosomal RNA spacer sequences as well as other RNA species.

Subunit interface

The surfaces of the small and large ribosomal subunits that face each other in functioning ribosomes.

Ribosome quality control complex

A complex that extracts nascent polypeptides from ribosomes that have stalled in translation.

E site

The specific binding site in ribosomes from which the deacylated (empty) tRNA exits from the ribosomes.

P site

The specific binding site in ribosomes for peptidyl-tRNA.

A site

The specific binding site in ribosomes for acceptor aminoacylated tRNA.

Beak structure

A structure in the small ribosomal subunit consisting of a protrusion of helix 33 of the 18S ribosomal bound by ribosomal proteins.

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Klinge, S., Woolford, J.L. Ribosome assembly coming into focus. Nat Rev Mol Cell Biol 20, 116–131 (2019). https://doi.org/10.1038/s41580-018-0078-y

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