The Structure and Function of the Eukaryotic Ribosome

Structures of the bacterial ribosome have provided a framework for understanding universal mechanisms of protein synthesis. However, the eukaryotic ribosome is much larger than it is in bacteria, and its activity is fundamentally different in many key ways. Recent cryo-electron microscopy reconstructions and X-ray crystal structures of eukaryotic ribosomes and ribosomal subunits now provide an unprecedented opportunity to explore mechanisms of eukaryotic translation and its regulation in atomic detail. This review describes the X-ray crystal structures of the Tetrahymena thermophila 40S and 60S subunits and the Saccharomyces cerevisiae 80S ribosome, as well as cryo-electron microscopy reconstructions of translating yeast and plant 80S ribosomes. Mechanistic questions about translation in eukaryotes that will require additional structural insights to be resolved are also presented.All ribosomes are composed of two subunits, both of which are built from RNA and protein (Figs. ​(Figs.11 and ​and2).2). Bacterial ribosomes, for example of Escherichia coli, contain a small subunit (SSU) composed of one 16S ribosomal RNA (rRNA) and 21 ribosomal proteins (r-proteins) (Figs. ​(Figs.1A1A and ​and1B)1B) and a large subunit (LSU) containing 5S and 23S rRNAs and 33 r-proteins (Fig. 2A). Crystal structures of prokaryotic ribosomal particles, namely, the Thermus thermophilus SSU (Schluenzen et al. 2000; Wimberly et al. 2000), Haloarcula marismortui and Deinococcus radiodurans LSU (Ban et al. 2000; Harms et al. 2001), and E. coli and T. thermophilus 70S ribosomes (Yusupov et al. 2001; Schuwirth et al. 2005; Selmer et al. 2006), reveal the complex architecture that derives from the network of interactions connecting the individual r-proteins with each other and with the rRNAs (Brodersen et al. 2002; Klein et al. 2004). The 16S rRNA can be divided into four domains, which together with the r-proteins constitute the structural landmarks of the SSU (Wimberly et al. 2000) (Fig. 1A): The 5′ and 3′ minor (h44) domains with proteins S4, S5, S12, S16, S17, and S20 constitute the body (and spur or foot) of the SSU; the 3′ major domain forms the head, which is protein rich, containing S2, S3, S7, S9, S10, S13, S14, and S19; whereas the central domain makes up the platform by interacting with proteins S1, S6, S8, S11, S15, and S18 (Fig. 1B). The rRNA of the LSU can be divided into seven domains (including the 5S rRNA as domain VII), which—in contrast to the SSU—are intricately interwoven with the r-proteins as well as each other (Ban et al. 2000; Brodersen et al. 2002) (Fig. 2A). Structural landmarks on the LSU include the central protuberance (CP) and the flexible L1 and L7/L12 stalks (Fig. 2A).Open in a separate windowFigure 1.The bacterial and eukaryotic small ribosomal subunit. (A,B) Interface (upper) and solvent (lower) views of the bacterial 30S subunit (Jenner et al. 2010a). (A) 16S rRNA domains and associated r-proteins colored distinctly: b, body (blue); h, head (red); pt, platform (green); and h44, helix 44 (yellow). (B) 16S rRNA colored gray and r-proteins colored distinctly and labeled. (C–E) Interface and solvent views of the eukaryotic 40S subunit (Rabl et al. 2011), with (C) eukaryotic-specific r-proteins (red) and rRNA (pink) shown relative to conserved rRNA (gray) and r-proteins (blue), and with (D,E) 18S rRNA colored gray and r-proteins colored distinctly and labeled.Open in a separate windowFigure 2.The bacterial and eukaryotic large ribosomal subunit. (A) Interface (upper) and solvent (lower) views of the bacterial 50S subunit (Jenner et al. 2010b), with 23S rRNA domains and bacterial-specific (light blue) and conserved (blue) r-proteins colored distinctly: cp, central protuberance; L1, L1 stalk; and St, L7/L12 stalk (or P-stalk in archeaa/eukaryotes). (B–E) Interface and solvent views of the eukaryotic 60S subunit (Klinge et al. 2011), with (B) eukaryotic-specific r-proteins (red) and rRNA (pink) shown relative to conserved rRNA (gray) and r-proteins (blue), (C) eukaryotic-specific expansion segments (ES) colored distinctly, and (D,E) 28S rRNA colored gray and r-proteins colored distinctly and labeled.In contrast to their bacterial counterparts, eukaryotic ribosomes are much larger and more complex, containing additional rRNA in the form of so-called expansion segments (ES) as well as many additional r-proteins and r-protein extensions (Figs. 1C–E and ​and2C–E).2C–E). Compared with the ∼4500 nucleotides of rRNA and 54 r-proteins of the bacterial 70S ribosome, eukaryotic 80S ribosomes contain >5500 nucleotides of rRNA (SSU, 18S rRNA; LSU, 5S, 5.8S, and 25S rRNA) and 80 (79 in yeast) r-proteins. The first structural models for the eukaryotic (yeast) ribosome were built using 15-Å cryo–electon microscopy (cryo-EM) maps fitted with structures of the bacterial SSU (Wimberly et al. 2000) and archaeal LSU (Ban et al. 2000), thus identifying the location of a total of 46 eukaryotic r-proteins with bacterial and/or archaeal homologs as well as many ES (Spahn et al. 2001a). Subsequent cryo-EM reconstructions led to the localization of additional eukaryotic r-proteins, RACK1 (Sengupta et al. 2004) and S19e (Taylor et al. 2009) on the SSU and L30e (Halic et al. 2005) on the LSU, as well as more complete models of the rRNA derived from cryo-EM maps of canine and fungal 80S ribosomes at ∼9 Å (Chandramouli et al. 2008; Taylor et al. 2009). Recent cryo-EM reconstructions of plant and yeast 80S translating ribosomes at 5.5–6.1 Å enabled the correct placement of an additional six and 10 r-proteins on the SSU and LSU, respectively, as well as the tracing of many eukaryotic-specific r-protein extensions (Armache et al. 2010a,b). The full assignment of the r-proteins in the yeast and fungal 80S ribosomes, however, only became possible with the improved resolution (3.0–3.9 Å) resulting from the crystal structures of the SSU and LSU from Tetrahymena thermophila (Klinge et al. 2011; Rabl et al. 2011) and the Saccharomyces cerevisiae 80S ribosome (Figs. ​(Figs.1D,E1D,E and ​and2D,E)2D,E) (Ben-Shem et al. 2011).