Factor‐Mediated Ribosome Assembly in Bacteria

Abstract

The ribosome is a structurally and functionally conserved macromolecular machine responsible for translating messenger ribonucleic acid (mRNA) into proteins. Composed of two independently assembled subunits, the bacterial ribosome is approximately 2.5 MDa in size. The process of translation, catalysed by the ribosome, is central to gene expression in the cell. Correspondingly, the regulation of ribosome biogenesis is paramount to cell viability, growth and differentiation. Moreover, the ribosome is the target of numerous clinically relevant therapeutic agents, several of which are known to affect ribosome assembly. Although, in vitro reconstitution of bacterial ribosomal subunits can be achieved using purified ribosomal RNA (rRNA) and r‐protein components, the process occurs at nonphysiological conditions. It is suggested that a specific order of processing and assembly events and regulatory factors is required to achieve fully functional particles. This article focuses on the protein factors that are involved in the process of bacterial ribosome biogenesis.

Key concepts:

  • This article focuses on the protein factors that are involved in the process of bacterial ribosome biogenesis.

Keywords: assembly; biogenesis; ribosome; RNA; translation; bacteria

Figure 1.

rRNA processing in bacteria. The rRNA operon in bacteria contains all three rRNAs, separated by noncoding sequences and tRNAs. Primary processing occurs at RNase III cleavage sites, formed by base pairing between sequences 5′ and 3′ to the rRNA sequence. In E. coli cleavage by RNase E (aided by RNase G) generates the mature 5′ end of 16S and 5S rRNA and cleavage by RNase T generates the mature 3′ end of 23S rRNA. The endonucleases for maturation of the 5′ end of 23S rRNA and the 3′ end of 16S and 5S rRNA remain unknown.

Figure 2.

Sites of methylation (red) and pseudouridinylation (yellow) are shown as spheres on the (a) small and (b) large ribosomal subunits. rRNA and r‐proteins are shown as ribbons in light and dark blue, respectively. In (a) a green ribbon indicates the path of the mRNA through the small subunit, whereas in (b) the antibiotic chloramphenicol (green) acts as a reference for peptidyltransferase centre on the large subunit. This figure was assembled from PDB accessions numbers 2AW4/7 (30S and 50S), 1YL3 (mRNA) and 1K01 (antibiotic) and is based on a figure from Decatur and Fournier .

Figure 3.

(a) Structure of RimM homologue from Pseudomonas aeruginosa (PDB2F1L), showing N‐ and C‐terminal domains (NTD, red and CTD, blue) with Y106 and Y107 indicated as sticks. (b) and (c) Location of RimM suppressor mutations in the E. coli 30S subunit (PDB2AW4). G1015A in h33b (orange), D974A in h31 (green), Δ89–99 in S13 (cyan) and R81 in S19 (blue) are shown with spheres. On the 30S subunit, the 5′ and 3′ termini of the 16S rRNA are indicated with a blue and red sphere, respectively. (d) An ensemble of 10 NMR structures of RbfA (PDB1KKG), with the helix‐turn‐helix (HTH) motif indicated in the KH‐domain, as well as the flexible C‐terminus. Note the 24 C‐terminal residues were not visualized, probably due to their flexible. (e) Cryo‐EM reconstruction of RbfA‐30S complex with 30S in yellow and extra density coloured red (Datta et al., ). (f) Proximity of the C‐terminus of RbfA (red) to helix 1 (h1, blue), central pseudoknot helix 27 (h27, orange) and helix 28 (h28, green) of 23S rRNA. (e) Reprinted from Datta et al. Structural aspects af RbfA action during small ribosomal subunit assembly. Molecular Cell28: 434–445. With permission from Elsevier.

Figure 4.

(a) 3D cryo‐EM map showing the binding position of Era (red) on the 30S subunit (yellow). The 30S subunit is shown in an interface view and a platform‐side view, respectively. (b) Model for the binding site of Era on the 30S subunit derived from cryo‐EM reconstructions (Sharma et al., ). The thumbnail shows birds‐eye view onto 30S subunit for orientation. Enlargement shows that the G‐domain of Era (red) interacts with r‐protein S2 (yellow), whereas the KH‐domain of Era (blue) contacts S11 (pink), S18 (orange) and S7 (not shown for clarity). In addition, the helix‐turn‐helix motif in the KH‐domain approaches the 3′ end of the 16S rRNA. The relative positions of A1518 and A1519 in helix 45 are also indicated. (c) Binding position of protein S1 (blue) in an interface view of the 30S subunit (yellow). In comparison with (a) Era and protein S1 show overlapping binding positions. (d) Structure of RsgA (YjeQ from Thermotoga maritima; Shin et al., ) highlighting the N‐terminal OB‐fold domain (blue), G‐domain (green) and C‐terminal zinc finger domain (orange). The Zn ion is shown as a red sphere. (a) and (c) Reproduced from Sharma et al. Interaction of Era with the 30S ribosomal subunit: implications for 30S subunit assembly. Molecular Cell18(3): 319–329. With permission from Elsevier.

Figure 5.

Structures of Obg from (a) T. thermophilus (PDB1UDX; Kukimoto‐Niino et al., ) and (b) B. subtilis (PDB1LNZ; Buglino et al., ) with (c) a superposition of both structures aligned on the basis of the unique OBG domain (green). In (a) the OCT domain (yellow) was also visualized, whereas in (b) the signalling molecule ppGpp was found in the G‐domain. The arrow in (c) indicates the different positions of the G‐domains relative to the OBG domain in the two structures. (d) Structure of T. maritimaDer (PDB1MKY; Robinson et al., ) coloured to highlight the C‐terminal KH‐domain (blue) and the two G‐domains (orange and green), which have GDP (blue) in the active sites. (e) Alignment of T. maritimaDer with B. subtilis homologue (PDB2HJG; Muench et al., ) on the basis of KH‐domain, revealing the dramatically different position of the G1 domains (arrowed). (f) and (g) structure of Der in (f) ‘open’ and (g) ‘closed’ conformations, shown as ribbons (above) and (h) and (i) as surface representation highlighting regions of positive and negative electrostatic potential in blue and red, respectively (below). Note the rearrangement of the G1 domain in the closed conformation covers the highly basic KH‐domain seen in the open conformation.

Figure 6.

(a) Structure of 4 in complex with GDPNP (magenta) (PDB1SVW; Ruzheinikov et al., ). Note, the highly basic Lys and Arg residues located in the C‐terminal (c) helix are also shown. (b) Binding site of RbgA (YlqF) on the large ribosomal subunit with enlargement of boxed area of inset subunit (with L1 (brown) and L11 (deep red) included for reference). (c) Ribosomal proteins L16 (orange), L25 (green) and L27 (blue) are highlighted, as are nucleotides C928 and C942 (magenta) in H38 (pink), A2301 (green) in H81 and A2354 (magenta) in H85. Figure uses B. subtilis numbering on D. radiodurans 50S structure as outlined by Matsuo et al.. (d) Crystal structure of RbgA (PDB1PUJ) indicating two domain arrangement, with N‐terminal G‐domain (blue) with GTP molecule (magenta) and C‐terminal acidic domain (green).

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Further Reading

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Williamson JR (2008) Biophysical studies of bacterial ribosome assembly. Current Opinion in Structural Biology 18: 299–304.

Woodson SA (2008) RNA folding and ribosome assembly. Current Opinion in Chemical Biology 12: 667–673.

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Dönhöfer, A, Sharma, MR, Datta, PP, Nierhaus, KH, Agrawal, RK, and Wilson, DN(Sep 2009) Factor‐Mediated Ribosome Assembly in Bacteria. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0021836]