Ribosomal Proteins: Their Role in the Assembly, Structure and Function of the Ribosome

Abstract

The ribosome is the macromolecular assembly dedicated to translating the genetic information into proteins. Ribosomes are made of several RNA molecules and between 50 and 80 proteins. The role played by these proteins has been the focus of investigations for over five decades. Initially, proteins were thought to be the only functional component of the ribosome, whereas the rRNA was considered merely a scaffold. This view has evolved and now is clear that both the RNA and protein components of the ribosome are functionally important. The r‐proteins play a role in the assembly process of the ribosome and are also essential for the structure and function of the ribosome. Their importance in the physiology of the ribosome is revealed by the fact that mutations in ribosomal proteins lead to ribosomopathies, a group of diseases that include developmental, haematological, metabolic and cardiovascular disorders, as well as cancers.

Key Concepts

  • The ribosome is a large macromolecular assembly dedicated to synthesising all proteins in all cells.
  • The ribosome in all domains of life is made of a small and a large subunit.
  • The small subunit decodes the genetic code and translate it into the sequence of amino acids that form a protein.
  • The large subunit is responsible for the peptide bond formation that links the amino acids in a functional protein.
  • The three core mechanisms of protein synthesis, including decoding and catalysis of peptide bond formation are performed by ribosomal ribonucleic acid (RNA).
  • The ribosome also contains 55–80 proteins.
  • During ribosomal assembly, the ribosomal proteins drive folding of ribosomal ribonucleic acid (rRNA).
  • In the mature ribosome, ribosomal proteins participate in the translation process, binding of translation factors and tuning ribosomal properties including translation fidelity.
  • Ribosomal proteins are also a useful tool to study how cellular proteins acquired their ability to fold over geological timescales.

Keywords: ribosome; ribosomal proteins; 80S; 70S; evolution; ribosome assembly factor; placeholder protein

Figure 1. Ribosomal proteins exhibit globular domains and long extensions. Proteins in the ribosome typically contain one or more globular domains that locate in the surface of the ribosome and long extensions that reach far into the internal parts of the ribosome. r‐Protein uS9 (a) and uL4 (b) from Bacillus subtilis showing this frequent topology. Reprinted from Sohmen et al. 2015 © Nature Communications distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/).
Figure 2. Structure and main landmarks of the bacterial ribosomal subunits. (a) Front (left) and back (right) views of the structure of the 30S subunit. Labels indicate the main landmarks of the ribosomal subunit and the r‐proteins. Panel (b) shows the ‘crown view’ (left) and solvent (right) view of the 50S subunit of Bacillus subtilis, respectively. Reprinted from Sohmen et al. 2015 © Nature Communications distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/)
Figure 3. Structure of the human 80S ribosome obtained by cryo‐electron microscopy. Cryo‐electron microscopy of the human 80S ribosome. The 40S subunit is shown in yellow and the 60S subunit is coloured in cyan. The background picture is an electron micrograph obtained by cryo‐electron microscopy using a Gatan K2 direct electron detector. Reprinted by permission from Macmillan Publishers Ltd: Nature (Khatter H, Myasnikov AG, Natchiar SK, Klaholz BP. Structure of the human 80S ribosome 520, 640–645), copyright 2015.
Figure 4. Gallery of ribosomal structures. A side‐by‐side comparison of the structures of the bacteria (E. coli) (PDB ID: 4v4q) (a), yeast (S. cerevisiae) (PDB ID: 4v88) (b) and human (PDB ID: 4ug0) (c) ribosomes. Panel (d) and (e) show the structures of the mitochondrial ribosome from human (PDB ID: 3j9m) and yeast (PDB ID: 5mrf), respectively.
Figure 5. Ribosomal proteins assist the folding of the rRNA during ribosomal assembly. A hypothetical folding landscape for the 50S ribosomal subunit. At the top of the energy funnel, the rRNA starts to fold. Binding of r‐proteins, simultaneously during folding, guides the rRNA folding and keeps it in a pathway leading to the correct structure. The r‐proteins are designated as primary when they bind directly to rRNA, secondary when binding is dependent on primary r‐proteins or tertiary for those when binding depends on secondary r‐proteins. The structure at the bottom represents the 50S subunit after reaching the mature state.
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Further Reading

Goudarzi KM and Lindstrom MS (2016) Role of ribosomal protein mutations in tumor development (Review). International Journal of Oncology 48: 1313–1324.

Kim TH, Leslie P and Zhang Y (2014) Ribosomal proteins as unrevealed caretakers for cellular stress and genomic instability. Oncotarget 5: 860–871.

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Razi, Aida, and Ortega, Joaquin(Sep 2017) Ribosomal Proteins: Their Role in the Assembly, Structure and Function of the Ribosome. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000535.pub2]