Ribosomal Proteins: Role in Ribosomal Functions

Rainer Nikolay, Charité ‐ Universitätsmedizin Berlin, Berlin, Germany
David van den Bruck, Max‐Delbrück‐Centrum für molekulare Medizin – Berlin Institute for Medical Systems Biology, Berlin, Germany
John Achenbach, NOXXON Pharma AG, Berlin, Germany
Knud H Nierhaus, Charité ‐ Universitätsmedizin Berlin, Berlin, Germany

Published online: June 2015

DOI: 10.1002/9780470015902.a0000687.pub4

Abstract

The assignment of specific ribosomal functions to individual ribosomal proteins is difficult due to the enormous cooperativity of the ribosome; however, important roles for distinct ribosomal proteins are becoming evident. Although ribosomal ribonucleic acid (rRNA) has the major claim to certain aspects of ribosome function, such as decoding and peptidyltransferase activity, there are also protein‐dominated functional hot‐spots on the ribosome such as the messenger RNA (mRNA) entry pore, the translation factor‐binding site and the exit of the ribosomal tunnel. The latter is binding site for both chaperones and complexes associated with protein transport through membranes. Furthermore, the contribution of ribosomal proteins is essential for the assembly and optimal functioning of the ribosome.

Key Concepts

  • A universal nomenclature for the ribosomal proteins was introduced in 2014, which terminates the babylonic chaos of the various nomenclature systems.
  • About two thirds of the bacterial ribosomal proteins have counterparts in archaeal and eukaryotic ribosomes.
  • Both rRNA and ribosomal proteins are essential for assembly, structure and function of the ribosomes.
  • A few ribosomal proteins are essential for the assembly, but lack a function in the mature ribosome.
  • In addition to rRNA‐dominated functional hot‐spots such as the decoding centre and the peptidyl‐transferase centre, there are also protein‐dominated functional hot‐spots such as the entry pore for the mRNA on the 30S subunit, the docking site for G‐protein factors and the exit of the tunnel harbouring the nascent peptide chain.

Keywords: ribosomal proteins, functions of; translational regulation; antibiotic resistance; mutant proteins; binding of translational factors

Figure 1. (a,b) New universal nomenclature according to Ban et al. () plus some more explanations.
Figure 2. Positions of ribosomal proteins in the T. thermophilus 30S (top) and 50S subunits (bottom). The rRNAs are in black, the ribosomal proteins are highlighted as coloured surface models. Next to uL11 should be uL10 and the bL12 stalk, which are not shown. 30S PDB file, 1N34 (Ogle et al., ); 50S PDB file, 2B66 (Petry et al., ).
Figure 3. The L1‐stalk makes a strong inward movement during intersubunit rotation: From an open position (blue) observed in the classical PRE‐state, the tip moves by 32 Å (measured at 23 rRNA nucleotide G2168) towards the intersubunit space. In the closed position of the hybrid PRE state (red), the L1‐stalk contacts the elbow of the P/E tRNA (green). The rest of the 50S subunit is shown in cyan, the unrotated 30S subunit (PRE classical) is shown in pale yellow and the rotated 30S subunit (PRE hybrid) in orange. The black dot marks the pivot point of the L1‐stalk movement. Coordinates from PDBs 3J0U and 3J0T (PRE classical) and 3J10 and 3J14 (PRE hybrid) (Agirrezabala et al., ).
Figure 4. Involvement of uS4, uS5 and uS12 during decoding. (a) Binding of cognate tRNA to the A site induces a transition in the 30S subunit from the open to the closed form. This involves a rotation of the head and movement of body (see arrows) towards the decoding site (anticodon–stem loop (ASL) of tRNA indicated (green) to indicate A site position). The closed‐form brings elements of uS12 (grey) and h44 (orange) into contact. (b) Serine 50 (Ser50) in the loop of uS12 monitors the correctness of the second position base pair of the A site codon–anticodon complex (U1 in the mRNA and A35 in the tRNA) by hydrogen bonding with A1492 of the 16S rRNA. (c) Ram mutations shown in orange and purple space‐fill representation that disrupt the interface between r‐proteins uS4 (cyan) and uS5 (blue) facilitate transition from the open to the closed form.
Figure 5. Ribosomal proteins located in the ribosomal tunnel and at the exit site. (a) Side view (from uL1 side) of 50S subunit highlighting r‐proteins uL4, uL22 and L23, the extensions of which reach into the tunnel (indicated by theoretical nascent polypeptide chain in yellow). (b) Close‐up of the ribosomal components at the tunnel kink, located adjacent to the PTF centre indicated with A (red) and P site (blue) ligands. The extensions of r‐proteins uL4 (orange) and uL22 (green) reach into the interior of the ribosome but do not come into contact with the macrolide erythromycin (ery) despite the fact that mutations (K63E in uL4) or deletions (82MEK84 in uL22) in these proteins confer resistance to this drug. Relief of the translational arrest caused by SecM resulting from mutation at positions Gly91 and Ala93 in uL22 (space filled in light green) and five nucleotide insertion at position A749 of the 23S rRNA. Mutations at position A2058 (purple) of the 23S rRNA confer resistance to erythromycin and relieve SecM translational arrest. The path of a hypothetical SecM nascent chain is shown with Pro (P) at the active site and Trp/Ile (WI) located in vicinity of the β‐hairpin of uL22. (c) View onto the tunnel exit from cytoplasmic side of 50S subunit showing the positions of the r‐proteins located at the exit site (white arrow). (d) The trigger factor (purple) with head, body and tail interacts via the latter with r‐protein uL23 at the exit site of the tunnel. The full‐length TF crystal structure has been docked on to the D50S subunit on the basis of the binding position of the N‐terminal‐binding domain (according to Schluenzen et al., ).
Figure 6. Position of the most conserved protein uL14 of the large ribosomal subunit. (a) 50S interface; CP, central proteberance. (b) uL14 position within the 70S ribosomes. Highly conserved amino acid residues at the surface in red.
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References

Agirrezabala X, Liao HY, Schreiner E, et al. (2012) Structural characterization of mRNA‐tRNA translocation intermediates. Proceedings of the National Academy of Sciences of the USA 109: 6094–6099.

Ban N, Beckmann R, Cate JH, et al. (2014) A new system for naming ribosomal proteins. Current Opinion in Structural Biology 24: 165–169.

Brodersen DE, Clemons WM Jr Carter AP, Wimberly BT and Ramakrishnan V (2002) Crystal structure of the 30S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16S RNA. Journal of Molecular Biology 316: 725–768.

Dabbs ER (1978) Mutational alterations in 50 proteins of the E. coli ribosomes. Molecular and General Genetics 165: 73–78.

Gumbart J, Schreiner E, Wilson DN, Beckmann R and Schulten K (2012) Mechanisms of SecM‐mediated stalling in the ribosome. Biophysical Journal 103: 331–341.

Halic M and Beckmann R (2005) The signal recognition particle and its interactions during protein targeting. Current Opinion in Structural Biology 15: 116–125.

Halic M, Blau M, Becker T, et al. (2006) Following the signal sequence from ribosomal tunnel exit to signal recognition particle. Nature 444: 507–511.

Harms JM, Wilson DN, Schluenzen F, et al. (2008) Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin. Molecular Cell 30: 26–38.

Häuser R, Pech M, Kijek J, et al. (2012) RsfA (YbeB) proteins are conserved ribosomal silencing factors. PLoS Genetics 8: e1002815.

Kaltschmidt E and Wittmann HG (1970) Ribosomal proteins XII. Number of proteins in the small and large ribosomal subunits of E. coli as determined by two‐dimensional gel electrophoresis. Proceedings of the National Academy of Sciences of the USA 67: 1276–1282.

Klein D, Moore P and Steitz T (2004) The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. Journal of Molecular Biology 340: 141–177.

Maier T, Ferbitz L, Deuerling E and Ban N (2005) A cradle for new proteins: trigger factor at the ribosome. Current Opinion in Structural Biology 15: 204–212.

Moore SD and Sauer RT (2008) Revisiting the mechanism of macrolide‐antibiotic resistance mediated by ribosomal protein L22. Proceedings of the National Academy of Sciences of the USA 105: 18261–18266.

Nakatogawa H and Ito K (2002) The ribosomal exit tunnel functions as a discriminating gate. Cell 105: 629–636.

Nierhaus KH (1991) The assembly of prokaryotic ribosomes. Biochimie 73: 739–755.

Ogle JM, Carter A and Ramakrishnan V (2003) Insights into the decoding mechanism from recent ribosome structures. TIBS 28: 259–266.

Ogle JM, Murphy FV IV Tarry M and Ramakrishnan V (2002) Selection of tRNA by the ribosome requires a translation from an open to a closed form. Cell 111: 721–732.

Petry S, Brodersen DE, Murphy FV IV et al. (2005) Crystal structure of the ribosoma in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell 123: 1255–1266.

Schluenzen F, Wilson DN, Tian P, et al. (2005) The binding mode of the trigger factor on the ribosome: implications for protein folding and SRP interaction. Structure 13: 1685–1694.

Shoji S, Dambacher CM, Shajani Z, Williamson JR and Schultz PG (2011) Systematic chromosomal deletion of bacterial ribosomal protein genes. Journal of Molecular Biology 413: 751–761.

Tenson T and Ehrenberg M (2002) Regulatory nascent peptides in the ribosomal tunnel. Cell 108: 591–594.

Uchiumi T, Honma S, Nomura T, Dabbs ER and Hachimori A (2002) Translation elongation by a hybrid ribosome in which proteins at the GTPase center of the E. coli ribosome are replaced with rat counterparts. Journal of Biological Chemistry 277: 3857–3862.

Further Reading

Brodersen D and Nissen P (2005) The social life of ribosomal proteins. FEBS Journal 272: 2098–2108.

Hill WE, Dahlberg A, Garrett RA, et al. (eds) (1990) The Ribosome: Structure, Function and Evolution. Washington, DC: American Society for Microbiology.

Nierhaus KH and Wilson DN (eds) (2004) Protein Synthesis and Ribosome Structure: Translating the Genome. Weinheim, Germany: Wiley‐VCH.

Noller HF and Nomura M (1996) Ribosomes. In: Neidhardt FC, Cortiss R III Ingraham JL, et al. (eds) E. coli and Salmonella. Washington, DC: ASM Press.

Ramakrishnan V (2014) The ribosome emerges from a black box. Cell 159: 979–984.

Wilson DN and Nierhaus KH (2005) Ribosomal proteins in the spotlight. Critical Reviews in Biochemistry and Molecular Biology 40: 243–267.

Wittmann H‐G (1982) Components of bacterial ribosomes. Annual Review of Biochemistry 51: 155–183.

Related Sub-Topics:

Proteins: Structure, Function, Metabolism | Information Flow | Translational Regulation | Cell Compartments and Cellular Organelles | Translation of RNA | Translation and Protein Synthesis | Biomolecular Interactions
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Article Title: Ribosomal Proteins: Role in Ribosomal Functions
 
How to Cite close
Nikolay, Rainer, van den Bruck, David, Achenbach, John, and Nierhaus, Knud H(Jun 2015) Ribosomal Proteins: Role in Ribosomal Functions. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000687.pub4]