Eukaryotic Ribosome Biogenesis: The 60S Subunit

Abstract

Ribosome biogenesis is consecutive coordinated maturation of ribosomal precursors in the nucleolus, nucleoplasm, and cytoplasm. The formation of mature ribosomal subunits involves hundreds of ribosomal biogenesis factors that ensure ribosomal RNA processing, tertiary structure, and interaction with ribosomal proteins. Although the main features and stages of ribosome biogenesis are conservative among different groups of eukaryotes, this process in human cells has become more complicated due to the larger size of the ribosomes and pre-ribosomes and intricate regulatory pathways affecting their assembly and function. Many of the factors involved in the biogenesis of human ribosomes have been identified using genome-wide screening based on RNA interference. A previous part of this review summarized recent data on the processing of the primary rRNA transcript and compared the maturation of the small 40S subunit in yeast and human cells. This part of the review focuses on the biogenesis of the large 60S subunit of eukaryotic ribosomes.

Keywords: biogenesis; nucleolus; ribosome; ribosomopathy.

Fig. 1

Structure and maturation of yeast pre-rRNA. (A) 25S rRNA contains six secondary structure domains (I–VI). 5.8S rRNA (shown in black) forms a complementary interaction with domain I of 25S rRNA (adapted from https://crw-site.chemistry.gatech.edu/). (B) Scheme of assembly of pre-60S pre-rRNA domains. The color coding of 25S rRNA domains is the same as in (A). Attachment of ribosomal proteins and biogenesis factors to the 35S rRNA precursor. The formation of the polypeptide exit tunnel (black circle) begins with binding of domain VI to domains I and II and a 5.8S region of the rRNA precursor. Folding of rRNA domains occurs in the following order: VI, V, III, and IV. In the F (final) state, domain V is completely folded [1]. (C) 5S rRNA turn [2]. (D) Secondary structures of yeast and human ITS1 and ITS2. Cleavage sites are marked with “V”. The predicted sites are indicated by question marks, and human exonuclease binding sites are underscored [3]. (E) Model of ITS2 processing by PNK RNase [4]. (F) Scheme of the interaction between the nuclear RNA exosome and pre-60S [5]. (G) Removal of ITS2 from the pre-60S particle by RNA processing enzymes. Intermediates formed during ITS2 removal are shown [6]

Fig. 2

Large ribosomal subunit assembly in yeast. Consecutive stages of large ribosomal subunit (60S) maturation are shown, starting with the earliest stages in the nucleolus, through stages in the nucleoplasm, and finally in the cytoplasm. rDNA regions giving rise to 5.8S rRNA, ITS2, domains I–VI of 25S rRNA, and 3’-ETS are indicated. Adapted from [14]. Assembly factors and complexes with known structures are depicted as cartoons; those whose structures are not known are indicated with text only

Fig. 3

Maturation pathways of the 35S pre-rRNA transcript in Saccharomyces cerevisiae (A) and the 47S pre-RNA transcript in Homo sapiens (C). Three of the four rRNAs (18S, 5.8S, and 25S (in yeast)/28S (in humans)) are synthesized by Pol I as a single long transcript. The coding sequences of mature rRNAs are flanked by 5’- and 3’-ETS, ITS1, and ITS2 non-coding spacers. The schematic shows the relative position of known and predicted cleavage sites. (B) Processing of pre-rRNA in budding yeast. (D) A simplified schematic of human pre-rRNA processing. The primary transcript, 47S pre-rRNA, is initially cleaved at both ends at sites 01 and 02 to form the 45S precursor that is processed via two alternative pathways [51]. “>” (e.g., C2>C1’>C1) denotes consecutive shortening of the appropriate 3’- or 5’-ends of the pre-rRNA by nucleases