Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome

Abstract

The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome, revealing how a network of biogenesis factors including 19 β-propellers and large α-solenoid proteins engulfs the pre-rRNA. Within the 90S pre-ribosome, we identify the UTP-A, UTP-B, Mpp10-Imp3-Imp4, Bms1-Rcl1, and U3 snoRNP modules, which are organized around 5'-ETS and partially folded 18S rRNA. The U3 snoRNP is strategically positioned at the center of the 90S particle to perform its multiple tasks during pre-rRNA folding and processing. The architecture of the elusive 90S pre-ribosome gives unprecedented structural insight into the early steps of pre-rRNA maturation. Nascent rRNA that is co-transcriptionally folded and given a particular shape by encapsulation within a dedicated mold-like structure is reminiscent of how polypeptides use chaperone chambers for their protein folding.

A Puzzle of Life: Crafting Ribosomal Subunits

“…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 ). Subsequently, the UTP-B complex binds downstream of UTP-A, but still within the 5 0 -ETS region.…”

“…A few of these preribosomal particles were visualized at relatively low resolution by EM [21][22][23][24]. Recent progress in cryo-EM has enabled a quantum jump by permitting the visualization of preribosomal particles at atomic or near-atomic resolution [25][26][27][28][29][30][31][32][33]. These studies not only provided a detailed view of the overall architecture of Glossary Biogenesis factors: the efficient and accurate assembly of ribosomal subunits is promoted by more than 200 proteins that are transiently associated with preribosomal particles; these proteins are collectively referred to as biogenesis factors, or alternatively as transacting or assembly factors.…”

“…Accordingly, in vivo purification of UTP-A or ÀB components permits the isolation of preribosomal particles comprising a 5 0 -ETS-containing pre-18S rRNA, about 20 SSU r-proteins, 65 biogenesis factors, and the U3 snoRNP [27,29]. A major recent breakthrough is the determination of cryo-EM structures of the 90S preribosome derived from Chaetomium thermophilum and S. cerevisiae [27,29,31] (Figure 4A).…”

“…Accordingly, in vivo purification of UTP-A or ÀB components permits the isolation of preribosomal particles comprising a 5 0 -ETS-containing pre-18S rRNA, about 20 SSU r-proteins, 65 biogenesis factors, and the U3 snoRNP [27,29]. A major recent breakthrough is the determination of cryo-EM structures of the 90S preribosome derived from Chaetomium thermophilum and S. cerevisiae [27,29,31] (Figure 4A). All three structures unveil the features of the nascent 40S moiety, revealing how most of the pre-rRNA, about 30 biogenesis factors, and 15 SSU r-proteins are arranged within this $5-MDa assembly intermediate [27,29,31].…”

“…A major recent breakthrough is the determination of cryo-EM structures of the 90S preribosome derived from Chaetomium thermophilum and S. cerevisiae [27,29,31] (Figure 4A). All three structures unveil the features of the nascent 40S moiety, revealing how most of the pre-rRNA, about 30 biogenesis factors, and 15 SSU r-proteins are arranged within this $5-MDa assembly intermediate [27,29,31]. The UTP-A and UTP-B modules are bound to the rRNA helices of the 5 0 ETS and form, together with the U3 snoRNP and additional biogenesis factors, a stable building block of the 90S preribosome.…”