Stage-specific assembly events of the 6-MDa small-subunit processome initiate eukaryotic ribosome biogenesis

2015 ◽  
Vol 22 (11) ◽  
pp. 920-923 ◽  
Author(s):  
Malik Chaker-Margot ◽  
Mirjam Hunziker ◽  
Jonas Barandun ◽  
Brian D Dill ◽  
Sebastian Klinge
Keyword(s):  
Ribosome Biogenesis ◽  
Small Subunit ◽  
Eukaryotic Ribosome

scholarly journals Utp14 Recruits and Activates the RNA Helicase Dhr1 To Undock U3 snoRNA from the Preribosome

2016 ◽  
Vol 36 (6) ◽  
pp. 965-978 ◽  
Author(s):  
Jieyi Zhu ◽  
Xin Liu ◽  
Margarida Anjos ◽  
Carl C. Correll ◽  
Arlen W. Johnson
Keyword(s):  
Ribosome Biogenesis ◽  
Rna Helicase ◽  
Small Subunit ◽  
Genetic Interactions ◽  
Base Pairs ◽  
Eukaryotic Ribosome ◽  
U3 Snorna ◽  
Stimulation Of

In eukaryotic ribosome biogenesis, U3 snoRNA base pairs with the pre-rRNA to promote its processing. However, U3 must be removed to allow folding of the central pseudoknot, a key feature of the small subunit. Previously, we showed that the DEAH/RHA RNA helicase Dhr1 dislodges U3 from the pre-rRNA.DHR1can be linked toUTP14, encoding an essential protein of the preribosome, through genetic interactions with the rRNA methyltransferase Bud23. Here, we report that Utp14 regulates Dhr1. Mutations within a discrete region of Utp14 reduced interaction with Dhr1 that correlated with reduced function of Utp14. These mutants accumulated Dhr1 and U3 in a pre-40S particle, mimicking a helicase-inactive Dhr1 mutant. This similarity in the phenotypes led us to propose that Utp14 activates Dhr1. Indeed, Utp14 formed a complex with Dhr1 and stimulated its unwinding activityin vitro. Moreover, theutp14mutants that mimicked a catalytically inactivedhr1mutantin vivoshowed reduced stimulation of unwinding activityin vitro. Dhr1 binding to the preribosome was substantially reduced only when both Utp14 and Bud23 were depleted. Thus, Utp14 is bifunctional; together with Bud23, it is needed for stable interaction of Dhr1 with the preribosome, and Utp14 activates Dhr1 to dislodge U3.

scholarly journals The small subunit processome in ribosome biogenesis-progress and prospects

2010 ◽  
Vol 2 (1) ◽  
pp. 1-21 ◽  
Author(s):  
Kathleen R. Phipps ◽  
J. Michael Charette ◽  
Susan J. Baserga
Keyword(s):  
Ribosome Biogenesis ◽  
Small Subunit

scholarly journals The Small Subunit Processome Is Required for Cell Cycle Progression at G1

2004 ◽  
Vol 15 (11) ◽  
pp. 5038-5046 ◽  
Author(s):  
Kara A. Bernstein ◽  
Susan J. Baserga
Keyword(s):  
Cell Cycle ◽  
Ribosome Biogenesis ◽  
Cell Cycle Progression ◽  
Small Subunit ◽  
Cellular Growth ◽  
Yeast Cells ◽  
G1 Phase ◽  
Relay Cell ◽  
Ssu Processome ◽  
Nucleolar Rna

Without ribosome biogenesis, translation of mRNA into protein ceases and cellular growth stops. We asked whether ribosome biogenesis is cell cycle regulated in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, and we determined that it is not regulated in the same manner as in metazoan cells. We therefore turned our attention to cellular sensors that relay cell size information via ribosome biogenesis. Our results indicate that the small subunit (SSU) processome, a complex consisting of 40 proteins and the U3 small nucleolar RNA necessary for ribosome biogenesis, is not mitotically regulated. Furthermore, Nan1/Utp17, an SSU processome protein, does not provide a link between ribosome biogenesis and cell growth. However, when individual SSU processome proteins are depleted, cells arrest in the G1 phase of the cell cycle. This arrest was further supported by the lack of staining for proteins expressed in post-G1. Similarly, synchronized cells depleted of SSU processome proteins did not enter G2. This suggests that when ribosomes are no longer made, the cells stall in the G1. Therefore, yeast cells must grow to a critical size, which is dependent upon having a sufficient number of ribosomes during the G1 phase of the cell cycle, before cell division can occur.

scholarly journals Release of the ribosome biogenesis factor Bud23 from small subunit precursors in yeast

RNA ◽  
2021 ◽  
pp. rna.079025.121
Author(s):  
Joshua J Black ◽  
Arlen W Johnson
Keyword(s):  
Binding Site ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Assembly Line ◽  
Small Subunit ◽  
Nucleotide Hydrolysis ◽  
Ribonucleoprotein Complexes ◽  
Intermediate States ◽  
Ssu Processome

Ribosomes are the universally conserved ribonucleoprotein complexes that synthesize proteins. The two subunits of the eukaryotic ribosome are produced through a quasi-independent assembly-line-like pathway involving the hierarchical actions of numerous trans-acting biogenesis factors and the incorporation of ribosomal proteins. The factors work together to shape the nascent subunits through a series of intermediate states into their functional architectures. The earliest intermediate of the small subunit (SSU or 40S) is the SSU Processome which is subsequently transformed into the pre-40S intermediate. This transformation is, in part, facilitated by the binding of the methyltransferase Bud23. How Bud23 is released from the resultant pre-40S is not known. The ribosomal proteins Rps0, Rps2, and Rps21, termed the Rps0-cluster proteins, and several biogenesis factors are known to bind the pre-40S around the time that Bud23 is released, suggesting that one or more of these factors induce Bud23 release. Here, we systematically examined the requirement of these factors for the release of Bud23 from pre-40S particles. We found that the Rps0-cluster proteins are needed but not sufficient for Bud23 release. The atypical kinase/ATPase Rio2 shares a binding site with Bud23 and is thought to be recruited to pre-40S after the Rps0-cluster proteins. Depletion of Rio2 prevented the release of Bud23 from the pre-40S. More importantly, the addition of recombinant Rio2 to pre-40S particles affinity-purified from Rio2-depleted cells was sufficient for Bud23 release in vitro. The ability of Rio2 to displace Bud23 was independent of nucleotide hydrolysis. We propose a novel role for Rio2 in which its binding to the pre-40S actively displaces Bud23 from the pre-40S, and we suggest a model in which the binding of the Rps0-cluster proteins and Rio2 promote the release of Bud23.

Requirements for the nuclear export of the small ribosomal subunit

2002 ◽  
Vol 115 (14) ◽  
pp. 2985-2995 ◽  
Author(s):  
Terence I. Moy ◽  
Pamela A. Silver
Keyword(s):  
Nuclear Export ◽  
Ribosome Biogenesis ◽  
Large Scale ◽  
Ribosomal Subunit ◽  
Small Subunit ◽  
Temperature Sensitive ◽  
Yeast Saccharomyces Cerevisiae ◽  
Small Ribosomal Subunit ◽  
Factors Affecting ◽  
The Stability

Eukaryotic ribosome biogenesis requires multiple steps of nuclear transport because ribosomes are assembled in the nucleus while protein synthesis occurs in the cytoplasm. Using an in situ RNA localization assay in the yeast Saccharomyces cerevisiae, we determined that efficient nuclear export of the small ribosomal subunit requires Yrb2, a factor involved in Crm1-mediated export. Furthermore, in cells lacking YRB2, the stability and abundance of the small ribosomal subunit is decreased in comparison with the large ribosomal subunit. To identify additional factors affecting small subunit export, we performed a large-scale screen of temperature-sensitive mutants. We isolated new alleles of several nucleoporins and Ran-GTPase regulators. Together with further analysis of existing mutants,we show that nucleoporins previously shown to be defective in ribosomal assembly are also defective in export of the small ribosomal subunit.

scholarly journals A Direct Interaction between the Utp6 Half-a-Tetratricopeptide Repeat Domain and a Specific Peptide in Utp21 Is Essential for Efficient Pre-rRNA Processing

2008 ◽  
Vol 28 (21) ◽  
pp. 6547-6556 ◽  
Author(s):  
Erica A. Champion ◽  
Bennett H. Lane ◽  
Meredith E. Jackrel ◽  
Lynne Regan ◽  
Susan J. Baserga
Keyword(s):  
Ribosome Biogenesis ◽  
Direct Interaction ◽  
Small Subunit ◽  
Tetratricopeptide Repeat ◽  
Peptide Ligand ◽  
Rrna Processing ◽  
Tetratricopeptide Repeat Domain ◽  
Domain Peptide ◽  
Ssu Processome ◽  
Specific Peptide

ABSTRACT The small subunit (SSU) processome is a ribosome biogenesis intermediate that assembles from its subcomplexes onto the pre-18S rRNA with yet unknown order and structure. Here, we investigate the architecture of the UtpB subcomplex of the SSU processome, focusing on the interaction between the half-a-tetratricopeptide repeat (HAT) domain of Utp6 and a specific peptide in Utp21. We present a comprehensive map of the interactions within the UtpB subcomplex and further show that the N-terminal domain of Utp6 interacts with Utp18 while the HAT domain interacts with Utp21. Using a panel of point and deletion mutants of Utp6, we show that an intact HAT domain is essential for efficient pre-rRNA processing and cell growth. Further investigation of the Utp6-Utp21 interaction using both genetic and biophysical methods shows that the HAT domain binds a specific peptide ligand in Utp21, the first example of a HAT domain peptide ligand, with a dissociation constant of 10 μM.

scholarly journals AtRsgA from Arabidopsis thaliana controls maturation of the small subunit of the chloroplast ribosome

2017 ◽  
Author(s):  
Marcin Janowski ◽  
Reimo Zoschke ◽  
Lars Scharff ◽  
Silvia Martinez Jaime ◽  
Camilla Ferrari ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Proteomic Analysis ◽  
Ribosome Biogenesis ◽  
Functional Characterization ◽  
Small Subunit ◽  
Signalling Pathways ◽  
Compensatory Mechanism ◽  
Transcriptional Responses ◽  
Retrograde Signalling ◽  
Assembly Factor

SummaryPlastid ribosomes are very similar in structure and function to ribosomes of their bacterial ancestors. Since ribosome biogenesis is not thermodynamically favourable at biological conditions, it requires activity of many assembly factors. Here, we have characterized a homolog of bacterial rsgA in Arabidopsis thaliana and show that it can complement the bacterial homolog. Functional characterization of a strong mutant in Arabidopsis revealed that the protein is essential for plant viability, while a weak mutant produced dwarf, chlorotic plants that incorporated immature pre-16S ribosomal RNA into translating ribosomes. Physiological analysis of the mutant plants revealed smaller, but more numerous chloroplasts in the mesophyll cells, reduction of chlorophyll a and b, depletion of proplastids from the rib meristem and decreased photosynthetic electron transport rate and efficiency. Comparative RNA-sequencing and proteomic analysis of the weak mutant and wild-type plants revealed that various biotic stress-related, transcriptional regulation and post-transcriptional modification pathways were repressed in the mutant. Intriguingly, while nuclear- and chloroplast-encoded photosynthesis-related proteins were less abundant in the mutant, the corresponding transcripts were upregulated, suggesting an elaborate compensatory mechanism, potentially via differentially active retrograde signalling pathways. To conclude, this study reveals a new chloroplast ribosome assembly factor and outlines the transcriptomic and proteomic responses of the compensatory mechanism activated during decreased chloroplast function.Significance statementAtRsgA is an assembly factor necessary for maturation of the small subunit of the chloroplast ribosome. Depletion of AtRsgA leads to dwarfed, chlorotic plants and smaller, but more numerous chloroplasts. Large-scale transcriptomic and proteomic analysis revealed that chloroplast-encoded and - targeted proteins were less abundant, while the corresponding transcripts were upregulated in the mutant. We analyse the transcriptional responses of several retrograde signalling pathways to suggest a mechanism underlying this compensatory response.

scholarly journals Nol12 is a multifunctional endonuclease at the nexus of RNA and DNA metabolism

2016 ◽  
Author(s):  
Daniel D Scott ◽  
Christian Trahan ◽  
Pierre-Joachim Zindy ◽  
Lisbeth-Carolina Aguilar ◽  
Marc Delubac ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
Genome Stability ◽  
Oxidative Dna Damage ◽  
Damage Identification ◽  
Alternative Pathway ◽  
Rna Metabolism ◽  
Small Subunit ◽  
Dna Helicase ◽  
P Bodies ◽  
Dna Maintenance

Endo- and exonucleases are major contributors to RNA metabolism through their diverse roles in maturation and turnover of different species of RNA as well as transcription. Recent data suggests RNA nucleases also affect genome stability programs and act along DNA repair pathways. Here, we describe Nol12 as a multifunctional RNA/DNA endonuclease found in different subcellular compartments - the nucleoplasm, where it co-localizes with the RNA/DNA helicase Dhx9 and paraspeckles, nucleoli as well as GW/P-bodies. We show that Nol12 is required for a key step in ribosomal RNA processing, separating large and small subunit precursors at site 2, rerouting ribosome biogenesis via an alternative pathway in its absence to ensure ribosome production. Furthermore, loss of Nol12 results in increased oxidized DNA levels followed by a rapid p53-independent ATR-Chk1-mediated apoptotic response, suggesting a role for Nol12 in the prevention or resolution of oxidative DNA damage. Identification of a complex Nol12 interactome, which includes NONO, Dhx9 and DNA-PK, further supports its diverse functions in RNA metabolism and DNA maintenance, establishing Nol12 as a multifunctional endonuclease.

scholarly journals snR30/U17 Small Nucleolar Ribonucleoprotein: A Critical Player during Ribosome Biogenesis

Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2195
Author(s):  
Timothy John Vos ◽  
Ute Kothe
Keyword(s):  
Ribosome Biogenesis ◽  
Current Knowledge ◽  
Small Subunit ◽  
Future Research ◽  
Unique Role ◽  
Ribosome Synthesis ◽  
Guide Rna ◽  
Guide Rnas ◽  
Ssu Processome ◽  
Nucleolar Rna

The small nucleolar RNA snR30 (U17 in humans) plays a unique role during ribosome synthesis. Unlike most members of the H/ACA class of guide RNAs, the small nucleolar ribonucleoprotein (snoRNP) complex assembled on snR30 does not direct pseudouridylation of ribosomal RNA (rRNA), but instead snR30 is critical for 18S rRNA processing during formation of the small subunit (SSU) of the ribosome. Specifically, snR30 is essential for three pre-rRNA cleavages at the A0/01, A1/1, and A2/2a sites in yeast and humans, respectively. Accordingly, snR30 is the only essential H/ACA guide RNA in yeast. Here, we summarize our current knowledge about the interactions and functions of snR30, discuss what remains to be elucidated, and present two non-exclusive hypotheses on the possible molecular function of snR30 during ribosome biogenesis. First, snR30 might be responsible for recruiting other proteins including endonucleases to the SSU processome. Second, snR30 may contribute to the refolding of pre-rRNA into a required conformation that serves as a checkpoint during ribosome biogenesis facilitating pre-rRNA cleavage. In both scenarios, the snR30 snoRNP may have scaffolding and RNA chaperoning activity. In conclusion, the snR30 snoRNP is a crucial player with an unknown molecular mechanism during ribosome synthesis, posing many interesting future research questions.

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