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Structural biology

Ribosome revelations

Proteins are synthesized in cells by the ribosome apparatus. A report of 16 yeast ribosome structures, each bound by a different inhibitor, broadens our understanding of how drugs affect ribosome activity. See Article p.517

The ribosome is the cellular machinery responsible for translating specific genetic codes into proteins by linking amino acids together, one by one. There are three types of ribosome: 70S, from prokaryotes (organisms whose cells do not have a nucleus, such as bacteria); 80S, from the cytoplasm of eukaryotes (organisms with nucleus-bearing cells, including fungi, plants and animals); and 55S, found in most eukaryotic mitochondria (the power plants of cells). On page 517 of this issue, Garreau de Loubresse et al.1 report 16 X-ray crystal structures of the 80S ribosome from the yeast Saccharomyces cerevisiae. Each structure reveals the binding mode for a distinct compound known to inhibit or modulate the protein-translation function of the ribosome. The authors' analysis provides a rationale for how most of these compounds exert their effects, and allows a comparison with analogous, previously reported structures of prokaryotic ribosomes.

Much like a precisely operating watch, the ribosome is a conglomerate of many parts, all of which are necessary for efficient function. It forms by the reversible association of a small and a large subunit. Two key regions are targets for clinically used antimicrobial agents and for compounds that ameliorate the symptoms of genetic diseases: the peptidyl transferase centre in the large subunit and the decoding centre in the small subunit. The chemistry conducted by the ribosome takes place in these centres. Garreau de Loubresse and colleagues find that the binding site of each compound in their structures is either within, or on the periphery of, the peptidyl transferase centre or the decoding centre (Fig. 1).

Figure 1: Binding sites of protein-translation inhibitors in the yeast ribosome.
figure1

Garreau de Loubresse et al.1 report 16 crystal structures of the yeast ribosome, each in complex with a different inhibitor of protein translation. The binding sites of these inhibitors (indicated by stars) span key regions associated with protein translation: the peptidyl site and the aminoacyl site (the binding sites of transfer RNA in the peptidyl transferase centre), and the tRNA exit site, all of which are in the large subunit; and the decoding centre and the messenger RNA tunnel of the small subunit. Colours of stars represent different classes of inhibitor.

Visualizing the three-dimensional positions of a compound interacting with its biological target is crucial for understanding the nature of the interactions and improving the compound's therapeutic value. Over the past decade, crystal structures of the 70S ribosome and its isolated subunits have been the most successful platform for studying compound–ribosome interactions at atomic resolution2,3. Through a combination of Garreau de Loubresse and co-workers' biophysical and biochemical experiments, we now have direct evidence for which surfaces in the chemical-activity centres of the eukaryotic 80S ribosome support the binding of compounds that affect protein translation. This evidence can be used in combination with previous advances4,5, and in parallel with further experimentation, to help design effective, non-toxic compounds for treating a variety of medical conditions, such as cystic fibrosis, tumour metastasis and severe haemophilia.

Perhaps the most interesting and revealing of Garreau de Loubresse and co-workers' results are those that focus on compounds that counter tumour proliferation in vitro6: the glutarimide compounds cycloheximide and lactimidomycin. Both of these inhibit protein synthesis by the 80S ribosome, but not by the 70S ribosome. The researchers' crystal structures identify the binding site for each compound at the exit of the peptidyl transferase centre. Comparisons with data for 70S structures7 show that the prokaryotic ribosome has components that occlude the glutarimide binding pocket, explaining these compounds' selectivity.

The authors' biochemical data also help to rationalize the different effects of each compound. Cycloheximide binds its ribosome pocket at any time during translation and blocks the exit of ribosome substrates from the peptidyl transferase centre. But the rate at which lactimidomycin binds its binding pocket is much lower than that of the substrates — so it cannot be accommodated in the ribosome during protein translation, but can bind and block the process before it starts. Because lactimidomycin is larger than cycloheximide, the authors propose that its binding is slower because of the extra effort needed to accommodate its greater bulk. In other words, when comparing the mechanism of action of the two compounds, size really does matter!

The inhibitor-bound structures reported by Garreau de Loubresse and colleagues are by no means the end of the road to understanding the selectivity and mechanism of action of drugs that target ribosomes. For example, because these structures lack both messenger RNA and transfer RNA, it remains to be seen how compounds such as edeine and cryptopleurine — which inhibit ribosome activity by interacting with mRNA and/or tRNA — affect protein translation at the ribosome.

As techniques for studying the ribosome improve, there will undoubtedly be quantum leaps in our understanding of how these machines work and in our ability to modulate their activity. Indeed, such a breakthrough8 was made earlier this year when cryoelectron microscopy (cryoEM) was used to visualize the 80S ribosome from the malaria-causing protozoan Plasmodium falciparum bound to the translation inhibitor emetine, at a resolution of 3.2 ångströms. This demonstrated that cryoEM can achieve sufficiently high resolution to distinguish the details of electrostatic-bond formation between ribosomes and bound compounds. Unlike X-ray crystallography, cryoEM does not need crystals9, so the ability to use cryoEM removes a major hurdle to structural studies of ribosomes.

In the meantime, by successfully clearing this hurdle, Garreau de Loubresse et al. have delivered groundbreaking data at atomic resolution that should further our understanding of how a diverse set of compounds affects the function of the 80s ribosome. It will be interesting to see which technique — X-ray crystallography or cryoEM — delivers the first 55S ribosome structure in the presence of an inhibitor.

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Correspondence to Nelson B. Olivier.

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Olivier, N. Ribosome revelations. Nature 513, 491–492 (2014). https://doi.org/10.1038/nature13747

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