The complete structure of the small-subunit processome

Barandun, Jonas; Chaker-Margot, Malik; Hunziker, Mirjam; Molloy, Kelly R.; Chait, Brian T.; Klinge, Sebastian

doi:10.1038/nsmb.3472

Cited by 121 publications

(161 citation statements)

References 55 publications

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“…Densities for all but one (rpS19) of these SSU r-proteins could be readily observed in recent cryo-EM analyses of purified yeast early nucleolar SSU precursors [46,47]. That is consistent with a direct role of these r-proteins in early SSU maturation steps.…”

Section: Introductionsupporting

confidence: 70%

Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors

Linnemann

Pöll

Jakob

et al. 2018

Preprint

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Many of the small ribosomal subunit proteins are required for the stabilisation of late small ribosomal subunit (SSU) precursors and for final SSU rRNA processing in S. cerevisiae. Among them are ribosomal proteins (r-proteins) which form a protein cluster around rpS0 (uS2) at the "neck" of the SSU (S0-cluster) and others forming a nearby protein cluster around rpS3 (uS3) at the SSU "beak". Here we applied semi-quantitative proteomics together with complementary biochemical approaches to study how incomplete assembly of these two r-protein clusters affects binding and release of SSU maturation factors and assembly of other r-proteins in late SSU precursors in S. cerevisiae. For each of the two clusters specific impairment of the local r-protein assembly state was observed. Besides, cluster-specific effects on the association of biogenesis factors were detected. These suggested a role of S0-cluster formation for the efficient release of the two nuclear export factors Rrp12 and Slx9 from SSU precursors and for the correct incorporation of the late acting biogenesis factor Rio2. Based on our and on previous results we propose the existence of at least two different r-protein assembly checkpoints during late SSU maturation in S. cerevisiae. We discuss in the light of recent SSU precursor structure models how r-protein assembly states might be sensed by biogenesis factors at the S0-cluster checkpoint.

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Section: Introductionsupporting

confidence: 70%

Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors

Linnemann

Pöll

Jakob

et al. 2018

Preprint

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“…As demonstrated previously, Rio1 serves the Ribi program by regulating 35S rDNA transcription, pre-rRNA processing and 40S ribosomal subunit maturation. However, we find that Rio1 also contributes by regulating the expression of 20% of the Ribi regulon members, including ORFs that encode components of the small subunit processome (122,123)) and proteins that mediate ribosome assembly, maturation, export, translation initiation and termination (Supplementary Table S5). Rio1 also physically interacts with proteins contributing to ribosome biogenesis and mRNA translation in events beyond those associated with Rio1 activity today.…”

Section: Discussionmentioning

confidence: 99%

Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae

Iacovella

Bremang

Basha

et al. 2018

Nucleic Acids Research

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The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subunit biogenesis and has not been characterized globally. We show that Rio1 manages directly and via a series of regulators, an essential signaling network at the protein, chromatin and RNA levels. Rio1 orchestrates growth and division depending on resource availability, in parallel to the nutrient-activated Tor1 kinase. To define the Rio1 network, we identified its physical interactors, profiled its target genes/transcripts, mapped its chromatin-binding sites and integrated our data with yeast’s protein–protein and protein–DNA interaction catalogs using network computation. We experimentally confirmed network components and localized Rio1 also to mitochondria and vacuoles. Via its network, Rio1 commands protein synthesis (ribosomal gene expression, assembly and activity) and turnover (26S proteasome expression), and impinges on metabolic, energy-production and cell-cycle programs. We find that Rio1 activity is conserved to humans and propose that pathological RIOK1 may fuel promiscuous transcription, ribosome production, chromosomal instability, unrestrained metabolism and proliferation; established contributors to cancer. Our study will advance the understanding of numerous processes, here revealed to depend on Rio1 activity.

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“…18, and as described below. DSS cross-linked nucleolar pre-60S particles in LDS buffer were reduced with 25 mM DTT, alkylated with 100 mM 2-chloroacetamide, separated by SDS–PAGE in three lanes of a 3–8% tris-acetate gel (NuPAGE, Thermo Fisher Scientific), and stained with Coomassie blue.…”

Section: Methodsmentioning

confidence: 99%

“…They further illustrate how the reduction of conformational freedom and ordered sequence of assembly factors are enforced during assembly. These are overarching themes of the nucleolar stages for both the small and large ribosomal subunit assembly 18 .…”

mentioning

confidence: 99%

Modular assembly of the nucleolar pre-60S ribosomal subunit

Sanghai

Miller

Molloy

et al. 2018

Nature

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137

165

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Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits1. A multitude of transient assembly factors regulate and chaperone the systematic folding of preribosomal RNA subdomains. However, owing to a lack of structural information, the role of these factors during early nucleolar 60S assembly is not fully understood. Here we report cryo-electron microscopy (cryo-EM) reconstructions of the nucleolar pre-60S ribosomal subunit in different conformational states at resolutions of up to 3.4 Å. These reconstructions reveal how steric hindrance and molecular mimicry are used to prevent both premature folding states and binding of later factors. This is accomplished by the concerted activity of 21 ribosome assembly factors that stabilize and remodel pre-ribosomal RNA and ribosomal proteins. Among these factors, three Brix-domain proteins and their binding partners form a ring-like structure at ribosomal RNA (rRNA) domain boundaries to support the architecture of the maturing particle. The existence of mutually exclusive conformations of these pre-60S particles suggests that the formation of the polypeptide exit tunnel is achieved through different folding pathways during subsequent stages of ribosome assembly. These structures rationalize previous genetic and biochemical data and highlight the mechanisms that drive eukaryotic ribosome assembly in a unidirectional manner.

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The complete structure of the small-subunit processome

Cited by 121 publications

References 55 publications

Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors

Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors

Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae

Modular assembly of the nucleolar pre-60S ribosomal subunit

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