rRNA Structure

Abstract

Ribosomal RNAs (rRNA) are essential components of ribosomes which are responsible for protein synthesis in all living cells. rRNA structure can be described at several levels – at the level of their primary sequences and secondary structures, as well as in terms of their tertiary folds of macromolecules within the ribosomal subunits.

Keywords: ribosome; RNA structure; translation; macromolecular structure

Figure 1.

16S ribosomal RNA. Sequences and secondary structures of the ribosomal RNAs from Escherichia coli. Symbols used: G–C, canonical base pair (A–U, G–C); G•U, G–U base pair; GoA, G–A base pair; U•U, noncanonical base pair. Every 10th nucleotide is marked with a tick mark and every 50th nucleotide is numbered. Tertiary interactions with strong comparative data are connected by solid lines. These secondary structure diagrams are adapted with permission from the Gutell Lab Comparative RNA Web Site [http://www.rna.icmb.utexas.edu]; Gutell RR (1996) In: Dahlberg AE and Zimmermann RA (eds) Ribosomal Structure, Evolution, Processing and Function in Protein Biosynthesis, pp. 111–128. Boca Raton: CRC Press. Extended helical segments are usually numbered sequentially from the 5′ end to the 3′ end of the RNA; only helical segments discussed in the text are marked on the figure.

Figure 2.

23S ribosomal RNA 5′ half. Sequences and secondary structures of the ribosomal RNAs from Escherichia coli. Symbols used: G–C, canonical base pair (A–U, G–C); G•U, G–U base pair; GoA, G–A base pair; U•U, noncanonical base pair. Every 10th nucleotide is marked with a tick mark and every 50th nucleotide is numbered. Tertiary interactions with strong comparative data are connected by solid lines. These secondary structure diagrams are adapted with permission from the Gutell Lab Comparative RNA Web Site [http://www.rna.icmb.utexas.edu]; Gutell RR (1996) In: Dahlberg AE and Zimmermann RA (eds) Ribosomal Structure, Evolution, Processing and Function in Protein Biosynthesis, pp. 111–128. Boca Raton: CRC Press. Extended helical segments are usually numbered sequentially from the 5′ end to the 3′ end of the RNA; only helical segments discussed in the text are marked on the figure.

Figure 3.

23S ribosomal RNA 3′ half. Sequences and secondary structures of the ribosomal RNAs from Escherichia coli. Symbols used: G–C, canonical base pair (A–U, G–C); G•U, G–U base pair; GoA, G–A base pair; U•U, noncanonical base pair. Every 10th nucleotide is marked with a tick mark and every 50th nucleotide is numbered. Tertiary interactions with strong comparative data are connected by solid lines. These secondary structure diagrams are adapted with permission from the Gutell Lab Comparative RNA Web Site [ http://www.rna.icmb.utexas.edu]; Gutell RR (1996) In: Dahlberg AE and Zimmermann RA (eds) Ribosomal Structure, Evolution, Processing and Function in Protein Biosynthesis, pp. 111–128. Boca Raton: CRC Press. Extended helical segments are usually numbered sequentially from the 5′ end to the 3′ end of the RNA; only helical segments discussed in the text are marked on the figure.

Figure 4.

5S ribosomal RNA. Sequences and secondary structures of the ribosomal RNAs from Escherichia coli. Symbols used: G–C, canonical base pair (A–U, G–C); G•U, G–U base pair; GoA, G–A base pair; U•U, noncanonical base pair. Every 10th nucleotide is marked with a tick mark and every 50th nucleotide is numbered. Tertiary interactions with strong comparative data are connected by solid lines. These secondary structure diagrams are adapted with permission from the Gutell Lab Comparative RNA Web Site [ http://www.rna.icmb.utexas.edu]; Gutell RR (1996) In: Dahlberg AE and Zimmermann RA (eds) Ribosomal Structure, Evolution, Processing and Function in Protein Biosynthesis, pp. 111–128. Boca Raton: CRC Press. Extended helical segments are usually numbered sequentially from the 5′ end to the 3′ end of the RNA; only helical segments discussed in the text are marked on the figure.

Figure 5.

Universal core secondary structure (grey‐shaded RNA sequences) and expansion segments (lightly shaded or unshaded rectangular boxes) of the 16S‐type ribosomal RNA. These regions are shown on the Escherichia coli 16S RNA secondary structure (see ) using conservation data from the Gutell Lab Comparative RNA Web Site [http://www.rna.icmb.utexas.edu]. The shaded parts of the secondary structure show nucleotide positions that are present in over 95% of 16S‐type rRNAs (the sequence itself will vary between organisms by compensatory base changes). Expansion segments that can vary in size from 10 to 50 nucleotides are shown as unshaded boxes, while segments that can vary by more than 50 nucleotides are shown as shaded boxes. The expansion segment around helix 21, for example, can vary in size from 0 to 842 nucleotides between different phylogenetic groups.

Figure 6.

Three‐dimensional structure of the Escherichia coli Sarcin/Ricin stem–loop (part of the 23S rRNA) illustrating some of the common structural motifs seen in RNA structure. The structure shown was derived using X‐ray crystallography by Correll CC, Wool IG and Munishkin A (1999) The two faces of the Escherichia coli 23S rRNA Sarcin/Ricin domain: the structure at 1.11 Å resolution. Journal of Molecular Biology292: 275–287. Two different views of this structure are shown as a ribbon diagram with only the RNA backbone and bases for clarity. The panel on the left looks into the major groove of the helical stem, while the right panel shows the minor groove face of the helical stem. Important structural motifs are marked and a secondary structure for the rRNA fragment is shown.

Figure 7.

Three‐dimensional fold of the ribosomal RNAs. (a) and (b) The crystallographic structure of the 16S rRNA from Thermus thermophilus derived by the group of V. Ramakrishnan (Wimberly BT et al. (2000) Structure of the 30S ribosomal subunit. Nature: 407: 327–339). A similar structure has been derived independently by the group of Ada Yonath. (c) and (d) The crystallographic structure of the 23S and 5S rRNAs in the 50S ribosomal subunit of Haloarcula marismortui derived by the groups of Peter Moore and Thomas Steitz (Ban N et al. (2000) The complete atomic structure of the large ribosomal subunit at 2.4Åresolution. Science289: 905–920). Panels (a) and (c) show a front view from the ribosomal subunit interface, while panels (b) and (d) show a side view with the subunit interface on the left side. For clarity, only the backbones of the RNAs are shown as a ribbon, without the ribosomal proteins. The RNA secondary structure domains are colour coded as follows: 30S subunit (panels a and b) – 5′ domain, red; central domain, green; 3′ major domain, yellow; and 3′ minor domain, blue. 50S subunit (panels c and d) – domain I, orange; domain II, blue; domain III, yellow; domain IV, green; domain V, red; domain VI, grey; and 5SrRNA, golden (as labelled).

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Further Reading

Ban N, Nissen P, Hansen J, Moore PB and Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289: 905–920.

Brimacombe R (1995) The structure of ribosomal RNA: a three‐dimensional jigsaw puzzle. European Journal of Biochemistry 230: 365–383.

Dahlberg AE and Zimmermann RA (eds) (1996) Ribosomal Structure, Evolution, Processing and Function in Protein Biosynthesis. Boca Raton, FL: CRC Press.

Garrett RA, Douthwaite SR, Liljas A et al. (eds) (2000) The Ribosome. Structure, Function, Antibiotics, and Cellular Interactions. Washington, DC: American Society for Microbiology Press.

Gutell RR, Larsen N and Woese CR (1994) Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiological Reviews 58: 10–26.

Hermann T and Patel DJ (1999) Stitching together RNA tertiary architectures. Journal of Molecular Biology 294: 829–849.

Noller HF (1984) Structure of ribosomal RNA. Annual Review of Biochemistry 53: 119–162.

Puglisi JD, Blanchard SC and Green R (2000) Approaching translation at atomic resolution. Nature Structural Biology 7: 855–861.

Schluenzen F, Tocilj A, Zarivach R et al. (2000) Structure of functionally activated small ribosomal subunit at 3.3 Å resolution. Cell 102: 615–623.

Wimberly BT, Brodersen DE, Clemons WM Jr et al. (2000) Structure of the 30S ribosomal subunit. Nature 407: 327–339.

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How to Cite close
Malhotra, Arun(May 2001) rRNA Structure. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0000537]