Escherichia coli K-12 substr. MG1655 Compound: 23S ribosomal RNA (rrlA)

Synonyms: rrlA

Superclasses: 23S rRNA

Component of: 50S ribosomal subunit

The 23S and 5S rRNAs are the RNA components of the large subunit (50S subunit) of the E. coli ribosome.

There are seven ribosomal RNA (rRNA) operons, called rrnA, rrnB, rrnC, rrnD, rrnE, rrnG, and rrnH. Each operon contains a 16S rRNA gene, a 23S rRNA gene, and a 5S rRNA gene (except the rrnD operon, which contains two 5S rRNA genes) interspersed with various tRNA genes. Regarding nomenclature, "rrs" genes encode 16S rRNAs, "rrl" genes encode 23S rRNAs, and "rrf" genes encode 5S rRNAs [Neidhardt96].

The sequence and structure of the 23S rRNA has been described, and the relationship of the 23S rRNA to ribosome assembly, structure, and function has been characterized. Interactions between the 23S rRNA and ribosomal proteins have been described.

The relationship of the 23S rRNA to sensitivity to multiple antibiotics is discussed. 23S rRNA also encodes a short peptide that plays a role in erythromycin resistance.

Analysis of mutations in 23S rRNA has been conducted.

The 23S rRNA is subject to pseudouridylation, dihydrouridylation, and methylation. Processing and modification of the 23S rRNA has been characterized. Possible roles for the modified nucleotides have been proposed [Sergiev07]; their location has been visualized in a cryo-EM structure of the ribosome [Fischer15].

Reviews describing these results are available.

Regulation has been described in detail; for a review see [Schneider03a].

Reviews: [Arthur87, BrissonNoel88, Dahlberg89, Srivastava91, Brimacombe91, Brimacombe92, Lane92, Mueller95, Wower95, Tenson95, Liebman95, Douthwalte95, Triman96, Triman97, Triman98, Triman99, Charette00, Nakajima99, Stark02a, Kim01].

Gene: rrlA Accession Numbers: EG30077 (EcoCyc), b3854, ECK3846

Sequence Length: 2902/3 AAs

Unification Links: EcoliWiki:b3854

Reactions known to consume the compound:

Not in pathways:
23S rRNA[periplasm] + H2O[periplasm] → 2 a single-stranded RNA[periplasm]

Not in pathways:
rRNA + S-adenosyl-L-methionine → rRNA containing N6,N6-dimethyladenine + S-adenosyl-L-homocysteine

Not in pathways:
23S rRNA[periplasm] + H2O[periplasm] → 2 a single-stranded RNA[periplasm]

Reactions known to produce the compound:

tRNA processing :
a tRNA precursor with a 5' extension and a short 3' extension + H2O → a tRNA precursor with a short 3' extension + a single-stranded RNA
a tRNA precursor with a 5' extension + H2O → an uncharged tRNA + a single-stranded RNA

Not in pathways:
YhaV endonuclease degradation substrate mRNA + H2O → 2 a single-stranded RNA
an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
RNase E degradation substrate mRNA + n H2O → n a single-stranded RNA
YhaV endonuclease degradation substrate rRNA + H2O → 2 a single-stranded RNA
RNase III mRNA processing substrate + 2 H2O → RNase III processing product mRNA + 2 a single-stranded RNA
an mRNA[periplasm] + H2O[periplasm] → 2 a single-stranded RNA[periplasm]
RNase G degradation substrate mRNA + H2O → 2 a single-stranded RNA
9S rRNA + 2 H2O → 5S rRNA + 2 a single-stranded RNA
RNase E mRNA processing substrate + n H2O → RNase E processing product mRNA + n a single-stranded RNA

Reactions known to both consume and produce the compound:

Not in pathways:
a single-stranded RNA + phosphate ↔ a single-stranded RNA + a nucleoside diphosphate

In Reactions of unknown directionality:

Not in pathways:
rRNA[periplasm] = 2 a single-stranded RNA[periplasm]

Not in pathways:
rRNA[periplasm] = 2 a single-stranded RNA[periplasm]

Enzymes inhibited by 23S ribosomal RNA (rrlA), sorted by the type of inhibition, are:

Inhibitor (Mechanism unknown) of: 3'-nucleotidase [Anraku64]

Gene-Reaction Schematic

Gene-Reaction Schematic

MultiFun Terms: cell structureribosomes
information transferprotein relatedtranslation
information transferRNA relatedrRNA, stable RNA


Anraku64: Anraku Y (1964). "A new cyclic phosphodiesterase having a 3'-nucleotidase activity from Escherichia coli B. II. Further studies on substrate specificity and mode of action of the enzyme." J Biol Chem 239;3420-4. PMID: 14245397

Arthur87: Arthur M, Brisson-Noel A, Courvalin P (1987). "Origin and evolution of genes specifying resistance to macrolide, lincosamide and streptogramin antibiotics: data and hypotheses." J Antimicrob Chemother 20(6);783-802. PMID: 3326871

Brimacombe91: Brimacombe R (1991). "RNA-protein interactions in the Escherichia coli ribosome." Biochimie 73(7-8);927-36. PMID: 1720671

Brimacombe92: Brimacombe R (1992). "Structure-function correlations (and discrepancies) in the 16S ribosomal RNA from Escherichia coli." Biochimie 74(4);319-26. PMID: 1379076

BrissonNoel88: Brisson-Noel A, Trieu-Cuot P, Courvalin P (1988). "Mechanism of action of spiramycin and other macrolides." J Antimicrob Chemother 22 Suppl B;13-23. PMID: 3053566

Charette00: Charette M, Gray MW (2000). "Pseudouridine in RNA: what, where, how, and why." IUBMB Life 49(5);341-51. PMID: 10902565

Dahlberg89: Dahlberg AE (1989). "The functional role of ribosomal RNA in protein synthesis." Cell 57(4);525-9. PMID: 2655923

Douthwalte95: Douthwalte S, Voldborg B, Hansen LH, Rosendahl G, Vester B (1995). "Recognition determinants for proteins and antibiotics within 23S rRNA." Biochem Cell Biol 73(11-12);1179-85. PMID: 8722035

Fischer15: Fischer N, Neumann P, Konevega AL, Bock LV, Ficner R, Rodnina MV, Stark H (2015). "Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM." Nature 520(7548);567-70. PMID: 25707802

Kim01: Kim DF, Semrad K, Green R (2001). "Analysis of the active site of the ribosome by site-directed mutagenesis." Cold Spring Harb Symp Quant Biol 66;119-26. PMID: 12762014

Lane92: Lane BG, Ofengand J, Gray MW (1992). "Pseudouridine in the large-subunit (23 S-like) ribosomal RNA. The site of peptidyl transfer in the ribosome?." FEBS Lett 302(1);1-4. PMID: 1587345

Liebman95: Liebman SW, Chernoff YO, Liu R (1995). "The accuracy center of a eukaryotic ribosome." Biochem Cell Biol 73(11-12);1141-9. PMID: 8722031

Mueller95: Mueller F, Doring T, Erdemir T, Greuer B, Junke N, Osswald M, Rinke-Appel J, Stade K, Thamm S, Brimacombe R (1995). "Getting closer to an understanding of the three-dimensional structure of ribosomal RNA." Biochem Cell Biol 73(11-12);767-73. PMID: 8721993

Nakajima99: Nakajima Y (1999). "Mechanisms of bacterial resistance to macrolide antibiotics." J Infect Chemother 5(2);61-74. PMID: 11810493

Neidhardt96: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low Jr KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE "Escherichia coli and Salmonella, Cellular and Molecular Biology, Second Edition." American Society for Microbiology, Washington, D.C., 1996.

Schneider03a: Schneider DA, Ross W, Gourse RL (2003). "Control of rRNA expression in Escherichia coli." Curr Opin Microbiol 6(2);151-6. PMID: 12732305

Sergiev07: Sergiev PV, Bogdanov AA, Dontsova OA (2007). "Ribosomal RNA guanine-(N2)-methyltransferases and their targets." Nucleic Acids Res 35(7):2295-301. PMID: 17389639

Srivastava91: Srivastava AK, Schlessinger D (1991). "Structure and organization of ribosomal DNA." Biochimie 73(6);631-8. PMID: 1764510

Stark02a: Stark H (2002). "Three-dimensional electron cryomicroscopy of ribosomes." Curr Protein Pept Sci 3(1);79-91. PMID: 12370013

Tenson95: Tenson T, Mankin A (1995). "Comparison of functional peptide encoded in the Escherichia coli 23S rRNA with other peptides involved in cis-regulation of translation." Biochem Cell Biol 73(11-12);1061-70. PMID: 8722022

Triman96: Triman KL (1996). "The 23S Ribosomal RNA Mutation Database (23SMDB)." Nucleic Acids Res 24(1);169-71. PMID: 8594571

Triman97: Triman KL, Adams BJ (1997). "Expansion of the 16S and 23S ribosomal RNA mutation databases (16SMDB and 23SMDB)." Nucleic Acids Res 25(1);188-91. PMID: 9016533

Triman98: Triman KL, Peister A, Goel RA (1998). "Expanded versions of the 16S and 23S ribosomal RNA mutation databases (16SMDBexp and 23SMDBexp)." Nucleic Acids Res 26(1);280-4. PMID: 9399853

Triman99: Triman KL (1999). "Mutational analysis of 23S ribosomal RNA structure and function in Escherichia coli." Adv Genet 41;157-95. PMID: 10494619

Wower95: Wower J, Wower IK, Kirillov SV, Rosen KV, Hixson SS, Zimmermann RA (1995). "Peptidyl transferase and beyond." Biochem Cell Biol 73(11-12);1041-7. PMID: 8722019

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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