The small subunit (SSU) processome is a 2.2 MDa ribonucleoprotein complex involved in the processing, assembly and maturation of the SSU of eukaryotic ribosomes. The identities of many of the factors involved in SSU biogenesis have been elucidated over the past 40 years. However, as our understanding increases, so do the number of questions about the nature of this complicated process. Cataloguing the components is the first step towards understanding the molecular workings of a system. This review will focus on how identifying components of ribosome biogenesis has led to the knowledge of how these factors, protein and RNA alike, associate with one another into sub-complexes, with a concentration on the small ribosomal subunit. We will also explore how this knowledge of sub-complex assembly has informed our understanding of the workings of the ribosome synthesis system as a whole. KeywordsSSU processome; U3 snoRNA; Utp; ribosomal SSU; RNA processing; RNA chaperoneThe process of making a single ribosome is a herculean task, and is one of the most metabolically expensive activities of a cell. In vigorously growing yeast cells, it requires the activity of all three RNA polymerases, accounting for 70% of total transcription, 90% of pre-mRNA splicing and more than 25% of translation.1 In Saccharomyces cerevisiae, nearly 7000 nucleotides of pre-rRNA must be accurately transcribed, cleaved, folded, chemically modified by 71 snoRNPs directing either 2′-O-methylation or pseudouridylation, and assembled with 78 ribosomal proteins (r-proteins) to form one mature ribosome. Despite the immensity of this task, about 2000 new ribosomes are produced each minute in yeast (~7500 subunits per minute in HeLa cells), leading to the presence of ~200 000 ribosomes in each cell (~10 million in each HeLa cell).1 , 2Because of its central importance, defects in ribosome biogenesis can have detrimental effects on cellular metabolism and vitality. Interestingly, a number of diseases have been found to be associated with defects in ribosome synthesis pathways. Several recent reviews contain details on the particular ribosomopathies known to date.3 , 4 In addition, ribosome biogenesis is a key component of the cell cycle where it regulates cell size and growth,5 -7 and is thus up-regulated in cancer.8 Despite this critical linkage, ribosome biogenesis is + To whom correspondence should be addressed. susan.baserga@yale.edu. * These two authors contributed equally NIH Public Access Author ManuscriptWiley Interdiscip Rev RNA. Author manuscript; available in PMC 2012 January 1. Published in final edited form as:Wiley Interdiscip Rev RNA. 2011 January ; 2(1): 1-21. doi:10.1002/wrna.57. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript understudied and its role in cancer is underappreciated. In addition, new evidence suggests that ribosome biogenesis proteins play critical roles in stem-cell differentiation in Drosophila.9 Furthermore, ribosome synthesis may also be a mechanism through which HIV modulates host respo...

The minor spliceosome is a ribonucleoprotein complex that catalyses the removal of an atypical class of spliceosomal introns (U12-type) from eukaryotic messenger RNAs. It was first identified and characterized in animals, where it was found to contain several unique RNA constituents that share structural similarity with and seem to be functionally analogous to the small nuclear RNAs (snRNAs) contained in the major spliceosome. Subsequently, minor spliceosomal components and U12-type introns have been found in plants but not in fungi. Unlike that of the major spliceosome, which arose early in the eukaryotic lineage, the evolutionary history of the minor spliceosome is unclear because there is evidence of it in so few organisms. Here we report the identification of homologues of minor-spliceosome-specific proteins and snRNAs, and U12-type introns, in distantly related eukaryotic microbes (protists) and in a fungus (Rhizopus oryzae). Cumulatively, our results indicate that the minor spliceosome had an early origin: several of its characteristic constituents are present in representative organisms from all eukaryotic supergroups for which there is any substantial genome sequence information. In addition, our results reveal marked evolutionary conservation of functionally important sequence elements contained within U12-type introns and snRNAs.

Maturation of the large ribosomal subunit (LSU) in eukaryotes is a complex and highly coordinated process that requires the concerted action of a large, dynamic, ribonucleoprotein complex, the LSU processome. While we know that >80 ribosome biogenesis factors are required throughout the course of LSU assembly, little is known about how these factors interact with each other within the LSU processome. To interrogate its organization and architecture, we took a systems biology approach and performed a semi-high-throughput, array-based, directed yeast two-hybrid assay. Assaying 4800 protein-protein interactions, we identified 232 high-confidence, binary-interacting protein pairs, representing a fourfold increase from current knowledge. The resulting LSU processome interactome map has enhanced our understanding of the organization and function of the biogenesis factors within the LSU processome, revealing both novel and previously identified subcomplexes and hub proteins, including Nop4.[Keywords: LSU processome; RNA; ribosome; yeast two-hybrid] Supplemental material is available for this article. Eukaryotic ribosomes are complex cellular machines that are comprised of four different ribosomal RNAs (rRNAs) and >70 ribosomal proteins (r-proteins) (Woolford and Baserga 2013). Ribosome assembly begins in the nucleolus with the transcription of the polycistronic pre-rRNA, termed the 35S in Saccharomyces cerevisiae, by RNA polymerase I. The 35S pre-rRNA undergoes numerous cleavage and modification steps to generate the mature 18S, 5.8S, and 25S rRNAs that are assembled with the r-proteins to form the small and large ribosomal subunits. Accurate and efficient production of ribosomes requires the coordinated activity of >150 biogenesis factors, including a number of proteins with enzymatic activity (Fatica and Tollervey 2002; Fromont-Racine et al.

SUMMARY Eukaryotic ribosome biogenesis requires hundreds of trans-acting factors and dozens of RNAs. Although most factors required for ribosome biogenesis have been identified, little is known about their regulation. Here, we reveal that the yeast deubiquitinating enzyme Ubp10 is localized to the nucleolus and that ubp10Δ cells have reduced pre-rRNAs, mature rRNAs, and translating ribosomes. Through proteomic analyses, we found that Ubp10 interacts with proteins that function in rRNA production and ribosome biogenesis. In particular, we discovered that the largest subunit of RNA polymerase I (RNAPI) is stabilized via Ubp10-mediated deubiquitination and that this is required in order to achieve optimal levels of ribosomes and cell growth. USP36, the human ortholog of Ubp10, complements the ubp10Δ allele for RNAPI stability, pre-rRNA processing, and cell growth in yeast, suggesting that deubiquitination of RNAPI may be conserved in eukaryotes. Our work implicates Ubp10/USP36 as a key regulator of rRNA production through control of RNAPI stability.