23S ribosomal RNA

The 23S rRNA is a 2904 nt long (in E. coli) component of the large subunit (50S) of the bacterial/archean ribosome. The ribosomal peptidyl transferase activity resides in domain V of this rRNA, and this domain is the most common binding site for antibiotics that inhibit translation. A well-known member of this antibiotic class, chloramphenicol, acts by inhibiting peptide bond formation, with recent 3D-structural studies showing two different binding sites depending on the species of ribosome. Linezolid and quinupristin-dalfopristin also bind to the 23S rRNA, and cross-resistance has been demonstrated between these antibiotics. Compared to 16S rRNA genes, 23S rRNA genes typically have higher sequence variations including insertions and/or deletions.[2]

Pseudoknot of the domain G(G12) of 23S ribosomal RNA
Predicted secondary structure and sequence conservation of PK-G12rRNA
Identifiers
SymbolPK-G12rRNA
RfamRF01118
Other data
RNA typeGene; rRNA
Domain(s)Bacteria
SO0001263
PDB structuresPDBe
A 3D representation of the ribosome. This is a view of the 3D arrangement of the 23S and 5S rRNA in the Escherichia coli 50S ribosomal subunit based on a cryo-electron microscopic reconstruction.[1]

The eukaryotic homolog of the 23S rRNA is the 28S ribosomal RNA, with a region filled by the 5.8S ribosomal RNA.[3]

23S rRNA Functions

In general, rRNA has an essential function of peptidyl transferase, the stimulating core of the ribosome plays role in the peptide bond configuration. Both peptidyl-tRNA and aminoacyl-tRNA are important for synthesizing protein and transpeptidation response. However, 23S rRNA positions which are G2252, A2451, U2506, and U2585 have a significant function for tRNA binding in P site of the large ribosomal subunit. These modification nucleotides in site P can inhibit peptidyl-tRNA from binding and also remains U2555 modification intervene with transferring peptidyl-tRNA to puromycin. Furthermore, the chemical modification of half of these positions G2251, G2253, A2439, and U2584 can not prevent the tRNA binding. Peptidyl-tRNA of 50s subunits which binds to the P site preserve eight positions of 23S rRNA from chemical modification. On the other hand, 23S rRNA impacts on mutation for cell growth. Mutations A1912G, A1919G and Ψ1917C have a powerful growth phenotypes and they prevent translation while mutation A1916G has a simple growth phenotype and it leads to defect in the 50S subunits.[4]

See also

References
  1. Mueller F, Sommer I, Baranov P, Matadeen R, Stoldt M, Wöhnert J, Görlach M, van Heel M, Brimacombe R (2000). "The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 Å resolution". J Mol Biol. 298 (1): 35–59. doi:10.1006/jmbi.2000.3635. PMID 10756104.
  2. Pei A, Nossa CW, Chokshi P, Blaser MJ, Yang L, Rosmarin DM, Pei Z, Stajich JE (5 May 2009). "Diversity of 23S rRNA Genes within Individual Prokaryotic Genomes". PLoS ONE. 4 (5): e5437. doi:10.1371/journal.pone.0005437. PMC 2672173. PMID 19415112.
  3. Doris, Stephen M.; Smith, Deborah R.; Beamesderfer, Julia N.; Raphael, Benjamin J.; Nathanson, Judith A.; Gerbi, Susan A. (October 2015). "Universal and domain-specific sequences in 23S–28S ribosomal RNA identified by computational phylogenetics". RNA. 21 (10): 1719–1730. doi:10.1261/rna.051144.115.
  4. Long KS, Munck C, Andersen TM, Schaub MA, Hobbie SN, Bottger EC, Vester B (9 August 2010). "Mutations in 23S rRNA at the Peptidyl Transferase Center and Their Relationship to Linezolid Binding and Cross-Resistance". Antimicrobial Agents and Chemotherapy. 54 (11): 4705–4713. doi:10.1128/AAC.00644-10. PMC 2976117. PMID 20696869.
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