Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome

Zhou, Yi; Musalgaonkar, Sharmishtha; Johnson, Arlen; Taylor, David W.

doi:10.1038/s41467-019-08880-0

Cited by 63 publications

(86 citation statements)

References 66 publications

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“…The maps allowed us to fit and refine atomic models for all six assembly states, including the biogenesis factors Arx1, Lsg1, Nmd3, Rei1, Reh1, eIF6, ribosomal proteins eL40, uL16 and uL11 together with the 5S, 5.8S and 25S rRNA (Figure 1B, Figure 1—figure supplements 2–4, Supplementary file 1A, B). In addition, we identified density corresponding to the phosphatase (Baßler et al, 2017) and zinc finger (Zhou et al, 2019) domains of Yvh1 situated between uL11 in the P-stalk and eIF6 (Figure 1A, states I-II).…”

Section: Resultsmentioning

confidence: 99%

“…Our study suggests that Yvh1 dissociates from the pre-60S particle prior to the binding of eL40 and uL16 (Figure 1A). However, while this work was under review, Yvh1 was reported to bind cytoplasmic pre-60S particles carrying eL40 and uL16 (Zhou et al, 2019). Perhaps explaining this discrepancy, our study has exclusively analysed native pre-60S particles, while Zhou et al examined particles purified from Rlp24-mutant cells or following treatment with the inhibitor diazaborine (Zhou et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

“…However, while this work was under review, Yvh1 was reported to bind cytoplasmic pre-60S particles carrying eL40 and uL16 (Zhou et al, 2019). Perhaps explaining this discrepancy, our study has exclusively analysed native pre-60S particles, while Zhou et al examined particles purified from Rlp24-mutant cells or following treatment with the inhibitor diazaborine (Zhou et al, 2019). Interpretation of the structural intermediates in the Zhou study should take also account of the heterogeneity in the deposited maps due to the classification strategy used.…”

Section: Discussionmentioning

confidence: 99%

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Mechanism of completion of peptidyltransferase centre assembly in eukaryotes

Kargas

Castro‐Hartmann

Escudero-Urquijo

et al. 2019

eLife

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During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase centre (PTC) completion that explains how integration of the last ribosomal proteins is coupled to release of the nuclear export adaptor Nmd3. Single-particle cryo-EM reveals that eL40 recruitment stabilises helix 89 to form the uL16 binding site. The loading of uL16 unhooks helix 38 from Nmd3 to adopt its mature conformation. In turn, partial retraction of the L1 stalk is coupled to a conformational switch in Nmd3 that allows the uL16 P-site loop to fully accommodate into the PTC where it competes with Nmd3 for an overlapping binding site (base A2971). Our data reveal how the central functional site of the ribosome is sculpted and suggest how the formation of translation-competent 60S subunits is disrupted in leukaemia-associated ribosomopathies.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Mechanism of completion of peptidyltransferase centre assembly in eukaryotes

Kargas

Castro‐Hartmann

Escudero-Urquijo

et al. 2019

eLife

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“…Recent developments in cryogenic-electron microscopy (cryo-EM) have shed a tremendous amount of light on the process of RP nuclear import and their incorporation into the ribosome. For further information on this aspect of ribosome biogenesis, the reader is encouraged to see the following publications: [12,14,15,16,17,18,19] (Figure 1).…”

Section: Ribosome Biogenesis: An Overviewmentioning

confidence: 99%

Signal Transduction in Ribosome Biogenesis: A Recipe to Avoid Disaster

Piazzi

Bavelloni

Gallo

et al. 2019

IJMS

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Energetically speaking, ribosome biogenesis is by far the most costly process of the cell and, therefore, must be highly regulated in order to avoid unnecessary energy expenditure. Not only must ribosomal RNA (rRNA) synthesis, ribosomal protein (RP) transcription, translation, and nuclear import, as well as ribosome assembly, be tightly controlled, these events must be coordinated with other cellular events, such as cell division and differentiation. In addition, ribosome biogenesis must respond rapidly to environmental cues mediated by internal and cell surface receptors, or stress (oxidative stress, DNA damage, amino acid depletion, etc.). This review examines some of the well-studied pathways known to control ribosome biogenesis (PI3K-AKT-mTOR, RB-p53, MYC) and how they may interact with some of the less well studied pathways (eIF2α kinase and RNA editing/splicing) in higher eukaryotes to regulate ribosome biogenesis, assembly, and protein translation in a dynamic manner.

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“…From the early nucleolar stage onwards, distinct maturation intermediates (pre-ribosomal particles) are characterized and classified by their association with specific maturation factors. Pioneering work from several laboratories has unveiled structural snapshots of several of these pre-60S precursor particles from yeast (Figure 2) [27,28,29,30,31,32,33,34,35,36,37]. Defining the structure and composition of these particles has uncovered the metamorphosis of the large ribosomal subunit during maturation; however, many gaps still remain in the blueprints of ribosome assembly (recently reviewed in [3,4,5,6]).…”

Section: Aaa-atpases In Ribosome Biogenesismentioning

confidence: 99%

Shaping the Nascent Ribosome: AAA-ATPases in Eukaryotic Ribosome Biogenesis

Prattes

Bergler

et al. 2019

Biomolecules

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AAA-ATPases are molecular engines evolutionarily optimized for the remodeling of proteins and macromolecular assemblies. Three AAA-ATPases are currently known to be involved in the remodeling of the eukaryotic ribosome, a megadalton range ribonucleoprotein complex responsible for the translation of mRNAs into proteins. The correct assembly of the ribosome is performed by a plethora of additional and transiently acting pre-ribosome maturation factors that act in a timely and spatially orchestrated manner. Minimal disorder of the assembly cascade prohibits the formation of functional ribosomes and results in defects in proliferation and growth. Rix7, Rea1, and Drg1, which are well conserved across eukaryotes, are involved in different maturation steps of pre-60S ribosomal particles. These AAA-ATPases provide energy for the efficient removal of specific assembly factors from pre-60S particles after they have fulfilled their function in the maturation cascade. Recent structural and functional insights have provided the first glimpse into the molecular mechanism of target recognition and remodeling by Rix7, Rea1, and Drg1. Here we summarize current knowledge on the AAA-ATPases involved in eukaryotic ribosome biogenesis. We highlight the latest insights into their mechanism of mechano-chemical complex remodeling driven by advanced cryo-EM structures and the use of highly specific AAA inhibitors.

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Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome

Cited by 63 publications

References 66 publications

Mechanism of completion of peptidyltransferase centre assembly in eukaryotes

Mechanism of completion of peptidyltransferase centre assembly in eukaryotes

Signal Transduction in Ribosome Biogenesis: A Recipe to Avoid Disaster

Shaping the Nascent Ribosome: AAA-ATPases in Eukaryotic Ribosome Biogenesis

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