Architecture of the yeast small subunit processome

Abstract

The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of nascent pre-ribosomal RNA (rRNA). Here, we present the cryo-electron microscopy structure of the yeast SSU processome at 5.1-angstrom resolution. The structure reveals how large ribosome biogenesis complexes assist the 5' external transcribed spacer and U3 small nucleolar RNA in providing an intertwined RNA-protein assembly platform for the separate maturation of 18S rRNA domains. The strategic placement of a molecular motor at the center of the particle further suggests a mechanism for mediating conformational changes within this giant particle. This study provides a structural framework for a mechanistic understanding of eukaryotic ribosome assembly in the model organism Saccharomyces cerevisiae.

A Puzzle of Life: Crafting Ribosomal Subunits

“…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.…”

“…Recent evidence strongly suggests that the 90S-associated Utp24 is the endonuclease responsible for cleavages at sites A 1 and A 2 [64]. This PIN-domain endonuclease is positioned in proximity to the A 1 cleavage site [27,29,64] and cleaves a pre-rRNA substrate at site A 2 in vitro [64]. A second 90S-associated endonuclease with in vitro A 2 cleavage activity is Rcl1 [27,29,31,65].…”