Ribosomes are the molecular machines that translate the genetic information contained within messenger RNAs into proteins. While there is a detailed understanding of eukaryotic ribosomes at both a structural and functional level [1–3]
, much less is known about the intricate assembly process of the ribosomal subunits. The biogenesis of ribosomes is initiated in the nucleolus by the transcription of a common large precursor of mature ribosomal RNAs. The nascent precursor rRNA (pre-rRNA), which undergoes snoRNP-mediated modification of nucleotides, assembles with some ribosomal proteins and early biogenesis factors to form the first pre-ribosomal particles. Concomitant to or shortly after completion of transcription, the pre-rRNA undergoes endonucleolytic cleavages that separate the precursor particles to the mature 40S and 60S ribosomal subunits. These pre-40S and pre-60S particles mature further in the nucleolus and nucleoplasm before being exported to the cytoplasm, where final maturation events yield the translation-competent ribosomal subunits [4–10]
. Proteomic analyses have identified many distinct pre-ribosomal particles that can be chronologically ordered along the maturation pathway from the nucleolus to the cytoplasm (). These landmark pre-ribosomal particles significantly differ in protein and (pre-)rRNA composition, thus highlighting the remarkable dynamics and complexity of shaping the rRNA and its associated ribosomal proteins into the correct structure.
Fig. 1 Biogenesis of the large (blue) and small (green) ribosomal subunit and the contribution of AAA-ATPases. Rix7, Rea1, and Drg1 are dedicated to the release and recycling of distinct biogenesis factors from different pre-60S particles. Major landmark of (more ...)
The combination of genetic, cell biological, and proteomic methods has revealed that more than 200, mostly essential, non-ribosomal factors (also called biogenesis factors or protein trans
-acting factors) contribute to eukaryotic ribosome biogenesis. While some of these factors are directly involved in the modification and processing of the pre-rRNA, others stabilize the pre-ribosomal particles, promote formation of productive RNA folding intermediates, or act as placeholders for selected ribosomal proteins that are recruited at a later time point in biogenesis. A further set of factors are essential for, or facilitate, the export of pre-ribosomes through the nuclear pore complex (NPC). A prominent number of biogenesis factors belong to different classes of energy-consuming enzymes, including ATP-dependent RNA helicases, GTPases, protein kinases, and three AAA-type ATPases [4,7]
. Nucleotide binding or hydrolysis by these enzymes is believed to be instrumental for the promotion or regulation of key biogenesis steps, thus conferring directionality and accuracy to the assembly process. For recent reviews on non-ribosomal factors and their functions during ribosome biogenesis, see [4,5,7]
In this review, we focus on the molecular roles of the AAA-ATPases (ATPases associated with various cellular activities) involved in ribosome biogenesis. To date, a role in this process could be attributed to three essential AAA-ATPases, namely Rix7 (ribosome export), Rea1/Mdn1 (ribosome export associated/midasin), and Drg1/Afg2 (diazaborine resistance gene/ATPase family gene), which act at distinct steps during 60S subunit biogenesis in the yeast Saccharomyces cerevisiae
. AAA-ATPases contain at least one structurally conserved ATPase module that assembles into functionally active ring structures. In addition to the conserved Walker A and Walker B motifs, they are characterized by class-specific elements that also contribute to ATP hydrolysis, such as the sensor-I, sensor-II and the arginine finger 
. Within these molecular machines, cycles of nucleotide binding and hydrolysis induce conformational changes that affect a broad range of substrate proteins [11,12]
While the AAA-ATPases Rix7 and Drg1 are closely related to the well-characterized Cdc48 (p97 in mammals), Rea1, which is the largest yeast protein, shares similarity to the microtubule motor protein dynein heavy chain (Dyn1). Interestingly, all three AAA-ATPases promote the release of distinct biogenesis factors from nucleolar (Nsa1 by Rix7), nucleolar and nucleoplasmic (Ytm1-Erb1-Nop7 and Rsa4 by Rea1) and cytoplasmic (several shuttling factors by Drg1) pre-60S intermediates () [13–16]
. The release of these factors from pre-60S particles ensures their recycling and likely triggers conformational changes that are critical determinants for the progression of ribosome assembly, e.g. promoting export or subunit-joining competence.