Ribosome Biogenesis in the YeastSaccharomyces cerevisiae

Abstract

Ribosomes are highly conserved ribonucleoprotein nanomachines that translate information in the genome to create the proteome in all cells. In yeast these complex particles contain four RNAs (.5400 nucleotides) and 79 different proteins. During the past 25 years, studies in yeast have led the way to understanding how these molecules are assembled into ribosomes in vivo. Assembly begins with transcription of ribosomal RNA in the nucleolus, where the RNA then undergoes complex pathways of folding, coupled with nucleotide modification, removal of spacer sequences, and binding to ribosomal proteins. More than 200 assembly factors and 76 small nucleolar RNAs transiently associate with assembling ribosomes, to enable their accurate and efficient construction. Following export of preribosomes from the nucleus to the cytoplasm, they undergo final stages of maturation before entering the pool of functioning ribosomes. Elaborate mechanisms exist to monitor the formation of correct structural and functional neighborhoods within ribosomes and to destroy preribosomes that fail to assemble properly. Studies of yeast ribosome biogenesis provide useful models for ribosomopathies, diseases in humans that result from failure to properly assemble ribosomes. TABLE OF CONTENTS Abstract 643Introduction 644

A Puzzle of Life: Crafting Ribosomal Subunits

“…The 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).…”

“…At the beginning of this millennium, the implementation of powerful in vivo affinity-purification approaches permitted the isolation and characterization of preribosomal particles [19,20]. Subsequently, the purification of additional preribosomal particles provided a detailed spatiotemporal picture of the preribosomal intermediates and their composition [5,9,14] (Figure 2). A few of these preribosomal particles were visualized at relatively low resolution by EM [21][22][23][24].…”

“…The transcription of rDNA and r-protein-encoding genes (RPGs) is connected to growth conditions, which are relayed via the TORC1 kinase [34], but a balanced production is complicated because the transcription of these components includes all three RNA polymerases [5,34]. While common promoter elements ensure the harmonized transcription of RPGs [34], a recent study revealed how a negative feedback loop links early assembly events with RPG transcription.…”

“…Already during rDNA transcription, the first biogenesis factors and r-proteins associate with the nascent 35S pre-rRNA to form the 90S preribosome/SSU processome [5,9,54]. Most of these biogenesis factors form well-defined complexes, including the U3 snoRNP and the [ 4 1 0 _ T D $ D I F F ] UTP-A, UTP-B, and UTP-C modules, which assemble in a stepwise manner with the pre-rRNA [5,55] ( Figure 2B).…”

“…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.…”