Roles of Dim2 in Ribosome Assembly

Abstract

In eukaryotes, ribosome assembly requires hundreds of conserved essential proteins not present in the mature particle. Despite their importance, the function of most factors remains unknown. This is because protein deletion often affects the composition of the entire particle. Additionally, many proteins are present in assembling ribosomes for extended times, which makes it difficult to pinpoint their role to a particular step. Here we have combined classical yeast biochemistry with experiments using recombinant proteins and RNA to study the role of Dim2 and its interaction with Nob1, the nuclease that generates the 3-end of 18 S rRNA. Analysis of Dim2 mutants in which the interaction with Nob1 is disrupted demonstrates that this interaction between Dim2 and Nob1 is essential for optimal growth, and RNA binding experiments show that Dim2 increases Nob1 RNA affinity. Furthermore, our data indicate that Dim2 helps regulate Nob1 cleavage activity at the 3-end of 18 S rRNA, as point mutants where this interaction is abolished in vitro accumulate pre-ribosomes containing Nob1 and 20 S rRNA in vivo. Interestingly, the site of interaction with Nob1 is mapped to the canonical RNA binding surface of a KH-like domain in Dim2, providing another example where an RNA-binding domain can be repurposed for protein interactions.Ribosome assembly in eukaryotes is a complex and highly regulated process that consumes much of the energy of an actively growing cell (1). Ribosome assembly begins with the transcription of the ribosomal RNAs (rRNAs), 3 three of which (18 S, 5.8 S, and 25 S) are produced as a single transcript (Fig. 1). During transcription, this RNA is extensively methylated at 2Ј-OH groups (2), and initial cleavages separate the rRNAs destined for the small and large ribosomal subunit (3). Data in the literature indicate that 18 S rRNA processing is initiated in the nucleolus by a non-essential cleavage step (termed A 0 ) in the region 5Ј to 18 S rRNA (5Ј-ETS), followed by the essential cleavages at sites A 1 (to generate the 5Ј-end of 18 S rRNA) and A 2 (to separate 18 S rRNA from 5.8 S and 25 S rRNA (4), Fig. 1). The final step of 18 S rRNA maturation is the cytoplasmic cleavage at site D to form the mature 3Ј-end of 18 S rRNA. This cleavage step is carried out by the PIN-domaincontaining nuclease Nob1 (5-8).Modification and cleavage of pre-rRNAs is integrated with rRNA folding and binding of ribosomal proteins via a large machinery. In yeast, this essential machinery comprises ϳ200 proteins, assembly factors that bind transiently to pre-ribosomal complexes. Despite their importance for assembling this essential biomolecule, in many cases their specific roles in ribosome biogenesis remain unknown. The function of enzymes can be dissected relatively easily, resulting in the identification of all rRNA-modifying enzymes as well as many of the nucleolytic enzymes, particularly in the 60 S pathway. In contrast, the function of the majority of the assembly factors is harder to study, as by sequence analysis many proteins ...

Structural Heterogeneity in Pre-40S Ribosomes

“…We next turned to the platform and attempted to localize the endonuclease Nob1 and its accessory factor Pno1, which together direct the final cleavage to produce mature 18S rRNA (Lamanna and Karbstein, 2009, 2011; Pertschy et al, 2009; Woolls et al, 2011). As with the interface, lower resolution density for these AFs led us to perform focused 3D classification, revealing two major maps that both had density corresponding to Pno1 but only one of which had density corresponding to Nob1 (Fig.…”

Quality control mechanisms during ribosome maturation

“…It is unlikely that formation of the decoding site in 80S-like ribosomes alone is sufficient to promote Nob1-dependent cleavage, as 18S rRNA formation is blocked in the absence of the ATPase Fap7, which is stalled in 80S-like complexes. Nevertheless, the absence of S14 and S1 in these assembly intermediates [29] could account for the lack of Nob1-dependent cleavage, plausible as S14 directly binds Nob1 [50], and S1 binds Pno1 [21], a regulator for Nob1 [58]. …”

Identification of the binding site of Rlp7 on assembling 60S ribosomal subunits in Saccharomyces cerevisiae

“…Scaffolding proteins contain predicted protein-protein interaction domains and are sometimes found in subcomplexes with other assembly factors (Miles et al 2005). RNA binding proteins are thought to stabilize or chaperone prerRNA folding (Granneman et al 2011;Young and Karbstein 2011), target other proteins to preribosomes (Woolls et al 2011;Young et al 2013), or act as placeholders for r-proteins (Rodriguez-Mateos et al 2009). …”