UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly

Hunziker, Mirjam; Barandun, Jonas; Petfalski, Elisabeth; Tan, Dongyan; Delan-Forino, Clémentine; Molloy, Kelly R.; Kim, Kelly H.; Dunn-Davies, Hywel; Shi, Yi; Chaker-Margot, Malik; Chait, Brian T.; Walz, Thomas; Tollervey, David; Klinge, Sebastian

doi:10.1038/ncomms12090

Cited by 66 publications

(87 citation statements)

References 48 publications

(86 reference statements)

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“…The protein-RNA interaction at nucleotide G66 matches exactly. The first crosslink site is also in agreement to UTP-A CRAC data recently reported in yeast, in which Utp4 was crosslinked to the yeast 5'-ETS around bases 70–90 [23]. In contrast to our data, Hunziker and colleagues did not assign a second 5'-ETS region further downstream for Utp4 interaction.…”

Section: Discussionsupporting

confidence: 92%

“…Although the resolution is limited, the double helical parts could be clearly assigned, guided by secondary structure predictions and previous biochemical data [23], and thus nucleotides in the connecting single stranded regions could be approximately placed. Strikingly and hitherto not known, helices 1 and 2 are coaxially stacked to form a single unit with the 5'-terminus of the RNA being hidden in the center of the merger.…”

Section: Resultsmentioning

confidence: 99%

“…Although this unusual parallel complementation of the last blade could have been an artefact of our cloning strategy, it apparently represents a specific protein-binding site for Utp8 within the UTP-A complex as deduced from interaction studies [12, 23, 25, 26] and placing the Utp4 structure in a cryo-EM density of the 90S pre-ribosome. Within UTP-A, Utp4 and Utp17 present double-propellers.…”

Section: Discussionmentioning

confidence: 99%

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Structural basis for 5'-ETS recognition by Utp4 at the early stages of ribosome biogenesis

et al. 2017

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Eukaryotic ribosome biogenesis begins with the co-transcriptional assembly of the 90S pre-ribosome. The ‘U three protein’ (UTP) complexes and snoRNP particles arrange around the nascent pre-ribosomal RNA chaperoning its folding and further maturation. The earliest event in this hierarchical process is the binding of the UTP-A complex to the 5'-end of the pre-ribosomal RNA (5'-ETS). This oligomeric complex predominantly consists of β-propeller and α-solenoidal proteins. Here we present the structure of the Utp4 subunit from the thermophilic fungus Chaetomium thermophilum at 2.15 Å resolution and analyze its function by UV RNA-crosslinking (CRAC) and in context of a recent cryo-EM structure of the 90S pre-ribosome. Utp4 consists of two orthogonal and highly basic β-propellers that perfectly fit the EM-data. The Utp4 structure highlights an unusual Velcro-closure of its C-terminal β-propeller as relevant for protein integrity and potentially Utp8 recognition in the context of the pre-ribosome. We provide a first model of the 5'-ETS RNA from the internally hidden 5'-end up to the region that hybridizes to the 3'-hinge sequence of U3 snoRNA and validate a specific Utp4/5'-ETS interaction by CRAC analysis.

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Section: Discussionsupporting

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Structural basis for 5'-ETS recognition by Utp4 at the early stages of ribosome biogenesis

et al. 2017

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“…Several recent studies have significantly advanced our understanding of these initial assembly events. Biochemical reconstitution and structural approaches revealed the architecture of the UTP-A and UTP-B modules [56][57][58][59][60]. Crosslinking analyses supported the idea that UTP-A is the first module to associate with the 5 0 -external transcribed spacer (ETS) region of the nascent 35S pre-rRNA [27,58] (Figures 1, 2B, and 3 ).…”

Section: Assembly Of the Ssumentioning

confidence: 72%

A Puzzle of Life: Crafting Ribosomal Subunits

Kressler

Hurt

Baßler

2017

Trends in Biochemical Sciences

164

127

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The biogenesis of eukaryotic ribosomes is a complicated process during which the transcription, modification, folding, and processing of the rRNA is coupled with the ordered assembly of $80 ribosomal proteins (r-proteins). Ribosome synthesis is catalyzed and coordinated by more than 200 biogenesis factors as the preribosomal subunits acquire maturity on their path from the nucleolus to the cytoplasm. Several biogenesis factors also interconnect the progression of ribosome assembly with quality control of important domains, ensuring that only functional subunits engage in translation. With the recent visualization of several assembly intermediates by cryoelectron microscopy (cryo-EM), a structural view of ribosome assembly begins to emerge. In this review we integrate these first structural insights into an updated overview of the consecutive ribosome assembly steps. Synopsis of Eukaryotic Ribosome AssemblyRibosomes are the molecular machines that translate the genetic information from the intermediary mRNA templates into proteins [1]. Eukaryotic 80S ribosomes comprise two unequal subunits that contain four different rRNAs and around 80 r-proteins ( Figure 1). The small 40S subunit (SSU) comprises the 18S rRNA and 33 r-proteins (referred to as RPS or S). The large 60S subunit (LSU) comprises the 25S/28S, 5.8S, and 5S rRNA and, in most eukaryotic species, 47 r-proteins (RPL or L); a notable exception is budding yeasts, which lack eL28The act of building a ribosome begins in the nucleolus, where the ribosomal DNA (rDNA) is transcribed into a long pre-rRNA precursor (35S pre-rRNA in yeast) and involves the ordered assembly of the r-proteins with the pre-rRNA, which is concomitantly processed into the mature rRNA species [5][6][7][8] (Figure 1 and Box 1). These assembly and processing events are tightly coupled and occur within preribosomal particles (see Glossary) that travel, as maturation progresses, from the nucleus across nuclear pore complexes (NPCs) to the cytoplasm, where they are ultimately converted into translation-competent ribosomal subunits [5,[9][10][11][12][13] (Figure 2, Key Figure). Given the gargantuan complexity of this process, it is unsurprising that the assembly of eukaryotic ribosomes strictly requires the assistance of a plethora (>200) of mostly essential ribosome biogenesis factors, which are also called trans-acting or assembly factors [5,14,15].Our current knowledge has been mainly obtained by studying ribosome biogenesis in the yeast Saccharomyces cerevisiae. Research conducted in the 1970s defined the r-protein composition of ribosomes, revealed the major pre-rRNA processing intermediates, and uncovered the existence of the 90S, 43S, and 66S preribosomal particles. The following 25 years witnessed the identification of numerous biogenesis factors and attributed functional roles TrendsCryoelectron microscopy analyses of the 90S preribosome show that the biogenesis factors create a casting mold that encloses the nascent pre-40S subunit.Structures of nuclear pre-60S particles reveal that a...

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“…The first step of ribosome synthesis is the transcription by RNA polymerase I (Pol I) of the 35S pre-rRNA, the initial RNA precursor that contains the sequences for the mature 18S, 5.8S, and 25S rRNAs (Woolford and Baserga 2013). The 35S pre-rRNA nucleates the formation of a large 90S particle (also referred to as 90S preribosome or small subunit processome) composed of the U3 small nucleolar ribonucleoprotein (U3 snoRNP) and approximately 70 trans-acting factors that bind to the nascent transcript in a stepwise manner (Dragon et al 2002;Grandi et al 2002;Gallagher et al 2004;Pérez-Fernández et al 2007, 2011Phipps et al 2011;Chaker-Margot et al 2015;Hunziker et al 2016;Kornprobst et al 2016;Zhang et al 2016). Within the 90S particle, the 35S pre-rRNA is cleaved in a spacer region located between the 18S and the 5.8S rRNAs to yield a pre-40S particle and a pre-60S particle that will follow separate maturation routes and render the 40S and 60S ribosomal subunits, respectively (Henras et al 2008;Kressler et al 2010;Thomson et al 2013;Woolford and Baserga 2013;Fernandez-Pevida et al 2014;Henras et al 2015;Nerurkar et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Focal accumulation of preribosomes outside the nucleolus during metaphase–anaphase in budding yeast

Moriggi

Gaspar

Nieto

et al. 2017

RNA

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Saccharomyces cerevisiae contains one nucleolus that remains intact in the mother-cell side of the nucleus throughout most of mitosis. Based on this, it is assumed that the bulk of ribosome production during cell division occurs in the mother cell. Here, we show that the ribosome synthesis machinery localizes not only in the nucleolus but also at a center that is present in the bud side of the nucleus after the initiation of mitosis. This center can be visualized by live microscopy as a punctate body located in close proximity to the nuclear envelope and opposite to the nucleolus. It contains ribosomal DNA (rDNA) and precursors of both 40S and 60S ribosomal subunits. Proteins that actively participate in ribosome synthesis, but not functionally defective variants, accumulate in that site. The formation of this body occurs in the metaphase-to-anaphase transition when discrete regions of rDNA occasionally exit the nucleolus and move into the bud. Collectively, our data unveil the existence of a previously unknown mechanism for preribosome accumulation at the nuclear periphery in budding yeast. We propose that this might be a strategy to expedite the delivery of ribosomes to the growing bud.

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UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly

Cited by 66 publications

References 48 publications

Structural basis for 5'-ETS recognition by Utp4 at the early stages of ribosome biogenesis

Structural basis for 5'-ETS recognition by Utp4 at the early stages of ribosome biogenesis

A Puzzle of Life: Crafting Ribosomal Subunits

Focal accumulation of preribosomes outside the nucleolus during metaphase–anaphase in budding yeast

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