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Escherichia coli K-12 substr. MG1655 Compound: 16S ribosomal RNA (rrsA)

Synonyms: rrsA

Superclasses: 16S-rRNAs

Component of: 30S ribosomal subunit (summary available)

Summary:
The 16S rRNA is the RNA component of the small subunit (30S subunit) of the E. coli ribosome.

There are seven ribosomal RNA (rRNA) operons, called rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, and rrsH. Each operon contains a 16S rRNA gene, a 23S rRNA gene, and a 5S rRNA gene (except the rrsD 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].

16S rRNA has been studied extensively. Its sequence and structure has been described, its relationship to ribosome assembly, structure, and function has been characterized, interactions between the 16S rRNA and ribosomal proteins have been described, mutants have been analyzed. 16S rRNA is subject to post-transcriptional processing, methylation, and pseudouridylation. Possible roles for the modified nucleotides have been proposed [Sergiev07].

The 16S rRNA is targeted by a number of antibiotic agents. The functional interactions between antibiotic sensitivity and 16S rRNA have been examined in detail.

Reviews describing these results are available.

Regulation has been described in detail; for a review see [Schneider03].

Reviews: [Ganoza77, Garrett77, Brimacombe78, Azad79, Thompson83, Woese83, Moore88, Brimacombe88, Dahlberg89, Stern89, Leclerc90, Craigen90, Srivastava91, Brimacombe91, Scheinman92, Brimacombe92, Laughrea94, Tuite94, Triman95, Triman94, Easterwood95, Mueller95, BrakierGingras95, Groisman95, Ehresmann95, Triman96, Triman97, Moore97, Altman97, Nagano97, Triman98, Ashraf97, Lee01a, Recht01]

Gene: rrsA Accession Numbers: EG30084 (EcoCyc), b3851, ECK3843

Sequence Length: 513 AAs

Unification Links: EcoliWiki:b3851

Reactions known to consume the compound:

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

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:
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
YhaV endonuclease degradation substrate mRNA + H2O → 2 a single-stranded RNA
RNase III mRNA processing substrate + 2 H2O → RNase III processing product mRNA + 2 a single-stranded RNA
23S rRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]
an mRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]
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[periplasmic space] = 2 a single-stranded RNA[periplasmic space]


rRNA[periplasmic space] = 2 a single-stranded RNA[periplasmic space]

Enzymes inhibited by 16S ribosomal RNA (rrsA), sorted by the type of inhibition, are:

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

Gene-Reaction Schematic: ?

MultiFun Terms: cell structure ribosomes
information transfer protein related translation
information transfer RNA related rRNA, stable RNA


References

Altman97: Altman RB, Abernethy NF, Chen RO (1997). "Standardized representations of the literature: combining diverse sources of ribosomal data." Proc Int Conf Intell Syst Mol Biol 5;15-24. PMID: 9322010

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

Ashraf97: Ashraf SS, Guenther R, Ye W, Lee Y, Malkiewicz A, Agris PF (1997). "Ribosomal binding of modified tRNA anticodons related to thermal stability." Nucleic Acids Symp Ser NIL(36);58-60. PMID: 9478206

Azad79: Azad AA (1979). "Intermolecular base-paired interaction between complementary sequences present near the 3' ends of 5S rRNA and 18S (16S) rRNA might be involved in the reversible association of ribosomal subunits." Nucleic Acids Res 7(7);1913-29. PMID: 94160

BrakierGingras95: Brakier-Gingras L, Pinard R, Dragon F (1995). "Pleiotropic effects of mutations at positions 13 and 914 in Escherichia coli 16S ribosomal RNA." Biochem Cell Biol 73(11-12);907-13. PMID: 8722006

Brimacombe78: Brimacombe R (1978). "The sequence of E. coli 16S ribosomal RNA." Nature 276(5687);445. PMID: 364316

Brimacombe88: Brimacombe R (1988). "The emerging three-dimensional structure and function of 16S ribosomal RNA." Biochemistry 27(12);4207-14. PMID: 3048381

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

Craigen90: Craigen WJ, Lee CC, Caskey CT (1990). "Recent advances in peptide chain termination." Mol Microbiol 4(6);861-5. PMID: 2215213

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

Easterwood95: Easterwood TR, Harvey SC (1995). "Modeling the structure of the ribosome." Biochem Cell Biol 73(11-12);751-6. PMID: 8721991

Ehresmann95: Ehresmann C, Philippe C, Westhof E, Benard L, Portier C, Ehresmann B (1995). "A pseudoknot is required for efficient translational initiation and regulation of the Escherichia coli rpsO gene coding for ribosomal protein S15." Biochem Cell Biol 73(11-12);1131-40. PMID: 8722030

Ganoza77: Ganoza MC (1977). "The Ayerst Award Lecture 1976. Novel factors in protein biosynthesis." Can J Biochem 55(4);267-81. PMID: 322825

Garrett77: Garrett RA, Ungewickell E, Newberry V, Hunter J, Wagner R (1977). "An RNA core in the 30S ribosomal subunit of Escherichia coli and its structural and functional significance." Cell Biol Int Rep 1(6);487-502. PMID: 346237

Groisman95: Groisman I, Engelberg-Kulka H (1995). "Translational bypassing: a new reading alternative of the genetic code." Biochem Cell Biol 73(11-12);1055-9. PMID: 8722021

Laughrea94: Laughrea M (1994). "Structural dynamics of translating ribosomes: 16S ribosomal RNA bases that may move twice during translocation." Mol Microbiol 11(6);999-1007. PMID: 8022290

Leclerc90: Leclerc D, Brakier-Gingras L (1990). "Study of the function of Escherichia coli ribosomal RNA through site-directed mutagenesis." Biochem Cell Biol 68(1);169-79. PMID: 1693518

Lee01a: Lee K, Holland-Staley CA, Cunningham PR (2001). "Genetic approaches to studying protein synthesis: effects of mutations at Psi516 and A535 in Escherichia coli 16S rRNA." J Nutr 131(11);2994S-3004S. PMID: 11694635

Moore88: Moore PB (1988). "Structure-function correlations in the small ribosomal subunit from Escherichia coli." Annu Rev Biophys Biophys Chem 17;349-67. PMID: 3293591

Moore97: Moore PB (1997). "The conformation of ribosomes and rRNA." Curr Opin Struct Biol 7(3);343-7. PMID: 9204275

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

Nagano97: Nagano K, Nagano N (1997). "[Mechanism of decoding mRNA in protein biosynthesis]." Yakugaku Zasshi 117(10-11);749-63. PMID: 9414588

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.

Recht01: Recht MI, Williamson JR (2001). "Thermodynamics and kinetics of central domain assembly." Cold Spring Harb Symp Quant Biol 66;591-8. PMID: 12762060

Scheinman92: Scheinman A, Atha T, Aguinaldo AM, Kahan L, Shankweiler G, Lake JA (1992). "Mapping the three-dimensional locations of ribosomal RNA and proteins." Biochimie 74(4);307-17. PMID: 1379075

Schneider03: 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

Stern89: Stern S, Powers T, Changchien LM, Noller HF (1989). "RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA." Science 244(4906);783-90. PMID: 2658053

Thompson83: Thompson JF, Hearst JE (1983). "Structure-function relations in E. coli 16S RNA." Cell 33(1);19-24. PMID: 6380748

Triman94: Triman KL (1994). "The 16S ribosomal RNA mutation database (16SMDB)." Nucleic Acids Res 22(17);3563-5. PMID: 7937058

Triman95: Triman KL (1995). "Mutational analysis of 16S ribosomal RNA structure and function in Escherichia coli." Adv Genet 33;1-39. PMID: 7484450

Triman96: Triman KL (1996). "The 16S ribosomal RNA mutation database (16SMDB)." Nucleic Acids Res 24(1);166-8. PMID: 8594570

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

Tuite94: Tuite MF, Stansfield I (1994). "Termination of protein synthesis." Mol Biol Rep 19(3);171-81. PMID: 7969105

Woese83: Woese CR, Gutell R, Gupta R, Noller HF (1983). "Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids." Microbiol Rev 47(4);621-69. PMID: 6363901


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Tue Nov 25, 2014, BIOCYC14B.