Ribosome

Ribosomes play a key role in protein synthesis, a process that is essential for life. Although bacterial and mammalian ribosomes are fairly similar, there are some key differences. For example, eukaryotic (e.g., mammalian) ribosomes are larger and more complex, consisting of a 60S large subunit and a 40S small subunit which form an 80S ribosome (Myasnikov et al., 2009). The prokaryotic ribosomes are smaller and composed of 50S and 30S subunits. Specific structural differences between prokaryotic and eukaryotic ribosomes allow the ribosome to serve as a target for drug action.

Bacterial ribosomes are a target for several different classes of antibiotics approved by the US FDA e.g., Aminoglycosides, Tetracyclines, Macrolides, Oxazolidinones, and Lincosamindes. Learn more about protein synthesis as a target for antibiotics.

Function

Ribosomes function as macromolecular machines for protein synthesis in cells. Instructions for protein synthesis come from the cell's genome, via messenger RNA (mRNA). Ribosomes
provide a platform where the mRNA binds and is read by specific transfer RNA (tRNA) attached to their cognate amino acids. As the tRNAs bind to the ribosome, they transfer their amino acid cargo to the growing peptide chain, thereby decoding the mRNA, and translating it into a specific protein. Translation is a dynamic biological process that has three major phases: initiation, elongation, and termination/recycling (Rodnina, 2018). Learn more about protein synthesis.

Structure

Translation is a dynamic biological process that has three major phases: initiation, elongation, and termination/recycling (Rodnina, 2018). Although prokaryotic and eukaryotic ribosomes are fairly similar, there are some key differences in their structures. For example, eukaryotic ribosomes are larger and more complex, consisting of a 60S large subunit and a 40S small subunit which form an 80S ribosome (Myasnikov et al., 2009). Other specific structural differences allow the prokaryotic ribosomes (of pathogenic bacteria) to be targeted by drug molecules.

Bacterial ribosomes are composed of two subunits, a large 50S subunit (LSU) and a small 30S subunit (SSU). Each subunit contains chains of proteins and ribosomal RNA (rRNA). In Escherichia coli, X-ray crystallography revealed that (Arnez & Wilson, 2016):
1. The large subunit consists of 33 protein chains which are colored dark blue
2. The large subunit consists of a 23S rRNA of 2904 nucleotides which is colored cornflower blue
3. The large subunit consists of a 5S rRNA of 115 nucleotides which is colored deep sky blue
4. The small subunit consists of 21 protein chains which are colored violet-red
5. The small subunit consists of a 16S rRNA of 1541 nucleotides which is colored pink

Figure 1. A ribbon representation of the subunits of the bacterial ribosome. The components of the large subunit are colored in shades of blue and the parts of the small subunit are shown in shades of pink (PDB ID: 4v9d, Dunkle et al., 2011).

Active Site

Each ribosome contains several important locations which are critical for translation (Vázquez-Laslop & Mankin, 2018):
1. The A-site (red) contains the decoding center. In this location, an mRNA codon is paired with a corresponding transfer RNA (tRNA) molecule
2. The P-site (orange) binds the tRNA attached to the polypeptide chain
3. The E-site (green) serves as the exit location for tRNA molecules
4. The decoding center is located in the A-site of the SSU and is where the anticodon of a tRNA is recognized by the codon of an mRNA
5. The peptidyl transferase center (PTC) is located in the LSU and catalyzes peptide bond formation and peptide release
6. The ribosomal exit tunnel is located inside the LSU and funnels the polypeptide chain out of the ribosome after synthesis in the PTC (not shown in Figure 2)

Learn more about how each of these parts plays a role in protein synthesis.

Figure 2. Important locations on the bacterial ribosome. All tRNA molecules (shown in green, orange, and red) and the mRNA molecule (shown in yellow) are shown in a surface representation (PDB ID: 4v6f, Jenner et al., 2010).

Pharmacological Implications

There are many antibiotic classes that target bacterial ribosomes and target the ribosome's key functions - i.e., they act at the (a) decoding center, (b) peptidyl transferase center, and (c) nascent peptide exit tunnel (Lin et al., 2018).

Antibiotics that bind to the small subunit of the ribosome act at the decoding center to either inhibit binding of the tRNA at the A-site (e.g., Tetracycline) or inhibit translocation of tRNA bound to the A-site leading to miscoding (e.g., Negamycin). Several aminoglycosides (e.g., streptomycin, paromomycin, and gentamicin) bind near the A-site to induce conformational changes leading to miscoding. Antibiotics that bind to the P and E sites in the small subunit inhibit translation (e.g., kasugamycin, pactamycin) or affect tRNA and mRNA translocation (e.g., amicoumacin A). Antibiotics that bind to the large subunit of the ribosome act at the peptidyl transferase center (e.g., chloramphenicol, linezolid) or within the nascent peptide exit tunnel (e.g., Macrolide antibiotics such as erythromycin, and streptogramins such as Synercid). Finally, some antibiotics (e.g., thiostrepton and micrococcin) interfere with translation factors like EF-Tu, EF-G and IF2.

Since many of these antibiotics are produced by microorganisms, they have mechanisms to protect themselves from these toxic substances (Lin et al., 2018). These intrinsic mechanisms of protection or resistance form the foundation for the acquired resistance in pathogens. Under selective pressure (resulting from the use of antibiotics) pathogenic bacteria may acquire these resistance genes on mobile elements, e.g., plasmids, transposons, or integrons to become resistant to specific antibiotics. Thus, of the various classes of antibiotics, some are not used clinically due to toxicity, serious side effects, or resistance.

References

Arenz, S., & Wilson, D. N. (2016). Bacterial protein synthesis as a target for antibiotic inhibition. Cold Spring Harbor Perspectives in Medicine, 6(9), a025361. https://doi.org/10.1101/cshperspect.a025361

Dunkle, J. A., Wang, L., Feldman, M. B., Pulk, A., Chen, V. B., Kapral, G. J., Noeske, J., Richardson, J. S., Blanchard, S. C., Cate, J. H. (2011). Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science (New York, N.Y.), 332(6032), 981–984. https://doi.org/10.1126/science.1202692 PDB ID: 4v9d

Jenner, L. B., Demeshkina, N., Yusupova, G., Yusupov, M. (2010). Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nature Structural & Molecular Biology, 17(5), 555–560. https://doi.org/10.1038/nsmb.1790 PDB ID: 4v6f

Lin, J., Zhou, D., Steitz, T. A., Polikanov, Y. S., Gagnon, M. G. (2018) Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design. Annu Rev Biochem. 87, 451-478. https://doi.org/10.1146/annurev-biochem-062917-011942

Myasnikov, A. G., Simonetti, A., Marzi, S., Klaholz, B. P. (2009). Structure-function insights into prokaryotic and eukaryotic translation initiation. Current Opinion in Structural Biology, 19(3), 300–309. https://doi.org/10.1016/j.sbi.2009.04.010

Rodnina M. V. (2018). Translation in prokaryotes. Cold Spring Harbor perspectives in biology, 10(9), a032664. https://doi.org/10.1101/cshperspect.a032664

Vázquez-Laslop, N., Mankin, A. S. (2018). How macrolide antibiotics work. Trends in Biochemical Sciences, 43(9), 668–684. https://doi.org/10.1016/j.tibs.2018.06.011