Powering through ribosome assembly

Abstract

Ribosome assembly is required for cell growth in all organisms. Classic in vitro work in bacteria has led to a detailed understanding of the biophysical, thermodynamic, and structural basis for the ordered and correct assembly of ribosomal proteins on ribosomal RNA. Furthermore, it has enabled reconstitution of active subunits from ribosomal RNA and proteins in vitro. Nevertheless, recent work has shown that eukaryotic ribosome assembly requires a large macromolecular machinery in vivo. Many of these assembly factors such as ATPases, GTPases, and kinases hydrolyze nucleotide triphosphates. Because these enzymes are likely regulatory proteins, much work to date has focused on understanding their role in the assembly process. Here, we review these factors, as well as other sources of energy, and their roles in the ribosome assembly process. In addition, we propose roles of energy-releasing enzymes in the assembly process, to explain why energy is used for a process that occurs largely spontaneously in bacteria. Finally, we use literature data to suggest testable models for how these enzymes could be used as targets for regulation of ribosome assembly.

FIGURE 1.

rRNA cleavage involves many steps and energy-consuming factors. (Red arrows) Endonucleolytic steps; (blue arrows) exonucleolytic steps. The steps are labeled with the name of the nuclease if known or suggested, or the name of the cleavage site. Cleavage at site A₂ requires prior cleavage at site A₁ (Venema and Tollervey 1999; Karbstein 2009), cleavage at site D requires prior cleavage at site A₂ (Karbstein 2009), and processing to site B_1S requires prior cleavage at site A₃ (Karbstein 2009). For simplicity, only the major 60S processing pathway is shown. (Cyan) Putative ATPases (for simplicity, DEAD-box proteins are omitted); (green) GTPases; (orange) kinases.

FIGURE 2.

Model for Rix7-catalyzed remodeling of pre-60S subunits. Nsa1 binds to pre-60S subunits containing 27SA rRNA; other early 60S assembly factors including Rrp5, Noc1, and Nop4 are also bound to this intermediate. Rix7 interacts with Nsa1, potentially only in the ubiquitinated/sumoylated form, to remove it from pre-ribosomes (directly or indirectly). Nsa1 removal coincides with loss of the early 60S assembly factors Rrp5, Noc1, and Nop4, and allows binding of the later 60S assembly factors Rsa4, Nop53, Spb1, Nog2, Sda1, Arx1, and Nug1. (Orange) Energy-consuming assembly factors; (yellow) other assembly factors; (blue) Nsa1; (red) Rix7.

FIGURE 3.

Model for a conformational change in the 3′-major domain of 18S rRNA induced by the methylase Nep1. snR57 binds to pre-18S rRNA (complex I) to methylate G1572, marked by an asterisk. This interaction prevents the formation of H33 in mature 18S ribosomes (shown in green in complex IV). Nep1 binds to the GCAACUU sequence upstream of H47 could displace snR57, consistent with suppression of the Nep1 deletion by deletion of snR57. The ensuing formation of H33 (shown in green) allows binding of Rps19 to its suggested site in H45, prior to dissociation of Nep1.

FIGURE 4.

Dissociation of snR30 leads to a conformational switch in pre-ribosomes. Interaction of snR30 (red) with expansion segment 6 (ES6) in 18S rRNA (Fayet-Lebaron et al. 2009) prevents the proposed interaction between ES6 and ES3 (green), as well as a suggested pseudoknot in ES6 (blue) (Alkemar and Nygard 2003, 2006).

FIGURE 5.

Late cytoplasmic assembly intermediates are regulated in multiple layers. (Blue) 40S subunits; (green) 60S subunits; (orange) energy-consuming assembly factors; (yellow) select other assembly factors. Phosphorylation of Enp1, Rps3, and Tif6, catalyzed by Hrr25, and subsequent dephosphorylation, are required for maturation and export of the 40S and 60S subunits, respectively. Nob1-dependent cleavage at the 3′-end of 18S rRNA is regulated by the kinases Rio1 and Rio2, and the ATPase Fap7. The binding site for the bacterial homolog of Dim1, KsgA, overlaps with the binding site for IF3, indicating that Dim1-containing ribosomes cannot initiate translation. Rli1 binds to both pre-ribosomes and eIF3, indicating a link between assembling and initiating ribosomes. Release of Tif6 requires binding of the Shwachman-Diamond protein Sdo1, perhaps to recruit the GTPase Ria1, which can remove Tif6 from ribosoms in vitro. In addition, Drg1 is required to release Tif6 from pre-ribosomes. Arb1 binds to pre-ribosomes containing Tif6, but also interacts with initiation factors, linking the ribosome assembly and translation machineries.