Escherichia coli K-12 substr. MG1655 RNA: rrfG 5S ribosomal RNA

Gene: rrfG Accession Numbers: EG30075 (EcoCyc), b2588, ECK2586

Synonyms: rrnG

Superclasses: 5S rRNA

Regulation Summary Diagram: ?

Regulation summary diagram for rrfG

The 5S and 23S 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 [Neidhardt96]. 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 [Neidhardt96]. 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 5S rRNA has been described [Brownlee67, Boedtker67, Monier68, Cantor68, Cramer68, Raacke68, Aubert68, Reynier69, Richards69, Lewis70, Vigne71, Richards72, Fox75, Marshall77, Bear77, Vigne77, Weidner77, Lewis77, Chen78, Luoma78, Wagner78, Apirion78, Rabin79, Appel79, Jagadeeswaran80, Kao80, Burns80, Marshall80, Bohm81, Fanning81, Ramstein81, Peattie81, Douthwaite81, Speek82, Hancock82, Fox82, Pieler82, Kime82, Matveev, Stiege82, Delihas82, Luoma82, Matveeva, Kime83, Kime83a, Nazar83, Moore83, Erdmann83, Leontis84, Pieler84, Kime84, Goringer84, Christensen85, Pieler85, Muller86, Leontis86, Leontis86a, Goringer86, Leontis86b, Lorenz87, Gewirth87, Nagano88, Davis89, Zhang89, Zhang89a, Lorenz, Metelev90, Johnson91, Nazar91, Brunel91, White92, Ciesiolka92, Ciesiollka92, Zhong94, Dallas, Barciszewska96, Grune96, Grune96a, Correll97, Dallas97, Leontis98, Shpanchenko98, Wohnert99, Stoldt99, Lu00, Iwase99, Mahara00].

The relationship of the 5S rRNA to ribosome assembly, structure, and function has been characterized [Morell68, Siddiqui68, Siddiqui69, Forget70, Feunteun71, Bellemare72, Erdmann72, Erdmann73, Delihas75, Dohme76, Schreiber79, Spierer79, Jagadeeswaran80, Kao80, Odom80, Digweed81, StofflerMeilick81, Pace82, Rohl82, Rohl82a, Pieler82, Parker83, Silberklang83, Chiam83, Tewari83, Brewer83, Dontsova94, Sergiev98, Shpanchenko98, Ostergaard98, Osswald99, Mueller00, Sergiev00].

Interactions between the 5S rRNA and ribosomal proteins have been described [Horne72, Bellemare73, Schulte75, Brosius75, Bitar75, Berger75, Chu76, Osterberg76, Bear77, Zimmermann78, Newberry78, Spierer78, Spierer78a, Douthwaite79, Garrett79, Newberry80, Fanning81, Maimets81, Peattie81, Speek82, Douthwaite82, Kime83a, Moore83, Huber84, Kime84a, Christiansen85, Szymkowiak85, Leontis86a, Gewirth88, Egebjerg89, Dontsova90, Osswald90, Barciszewska96, Shpanchenko96, Stoldt99, Lu00, Okada00, Perederina02].

Interactions between the 5S rRNA and 23S rRNA have been described [Gray72, Herr75, Newberry80, Ostergaard98].

Analysis of mutations in 5S rRNA has been conducted [Pace82, Goringer84a, Goringer86a, Gewirth87a, Vester88, Gewirth88, Zhang89b, Zvereva98, Ammons99, Ammons01].

The post-transcriptional processing of the 5S rRNA has been characterized [Galibert69, Forget70a, Galibert71, Lund77, Ghora78, Ghora79, Goldblum81, Clark84, Szeberenyi84, Christiansen88, Melefors91, Georgellis92, Cormack92, Cormack93, Carpousis94, Li95, Bessarab98, Kaberdin00, Lee02a, Zuo02].

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

Reviews [Lind78, Azad79, Tanaka85, Nowotny88, Moore88, Vester88, Goringer88, Srivastava91, Barciszewska96, Barciszewska97].

Citations: [Robins68, Scott68, Jordan69, Feunteun70, Kaiser70, Doolittle70, Jarry71, Philipps72, Aubert73, Yu73, Garrett74, Hernandez75, Yuan75, Gorelic78, Glotz81, Schulze82, Karpel82, Kakegawa86, Abdukaiumov87, Teixido89, Kim91a, Merryman99, Usary01, Murphy01, Jarry70, Pace71, Doctor72, Jarry73, Jarry73a, Fraser75, Yamamoto76, Muto77, Shen77, Vola77, Morgan78, Bailey79, Duester80, Sarmientos83, Brosius84, Liebke85, Steen86, Seol90, Albrechtsen91, Orosz91]

Map Position: [2,724,091 <- 2,724,210] (58.71 centisomes, 211°)
Length: 120 bp

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:

Not in pathways:
9S rRNA + 2 H2O → 5S rRNA + 2 a single-stranded RNA

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
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]

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

Genetic Regulation Schematic: ?

Genetic regulation schematic for rrfG

Unification Links: ASAP:ABE-0008519 , CGSC:205 , EchoBASE:EB4238 , EcoGene:EG30075 , EcoliWiki:b2588 , OU-Microarray:b2588 , PortEco:rrfG , RegulonDB:EG30075

GO Terms:

Biological Process: GO:0006412 - translation
Cellular Component: GO:0005737 - cytoplasm
GO:0022625 - cytosolic large ribosomal subunit

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

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b2588 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG30075.


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Chen78: Chen MC, Giege R, Lord RC, Rich A (1978). "Raman spectra of ten aqueous transfer RNAs and 5S RNA. Conformational comparison with yeast phenylalanine transfer RNA." Biochemistry 17(15);3134-8. PMID: 359039

Chiam83: Chiam CL, Wagner R (1983). "Composition of the Escherichia coli 70S ribosomal interface: a cross-linking study." Biochemistry 22(5);1193-200. PMID: 6340734

Christensen85: Christensen A, Mathiesen M, Peattie D, Garrett RA (1985). "Alternative conformers of 5S ribosomal RNA and their biological relevance." Biochemistry 24(9);2284-91. PMID: 2581611

Christiansen85: Christiansen J, Douthwaite SR, Christensen A, Garrett RA (1985). "Does unpaired adenosine-66 from helix II of Escherichia coli 5S RNA bind to protein L18?." EMBO J 4(4);1019-24. PMID: 2990903

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Ciesiollka92: Ciesiollka J, Lorenz S, Erdmann VA (1992). "Different conformational forms of Escherichia coli and rat liver 5S rRNA revealed by Pb(II)-induced hydrolysis." Eur J Biochem 204(2);583-9. PMID: 1541274

Clark84: Clark MW, Lake JA (1984). "Unusual rRNA-linked complex of 50S ribosomal subunits isolated from an Escherichia coli RNase III mutant." J Bacteriol 157(3);971-4. PMID: 6199344

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Cramer68: Cramer F, Erdmann VA (1968). "Amount of adenine and uracil base pairs in E. coli 23S, 16S and 5S ribosomal RNA." Nature 217(136);92-3. PMID: 4868442

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Dallas97: Dallas A, Moore PB (1997). "The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins." Structure 5(12);1639-53. PMID: 9438864

Davis89: Davis DR, Yamaizumi Z, Nishimura S, Poulter CD (1989). "15N-labeled 5S RNA. Identification of uridine base pairs in Escherichia coli 5S RNA by 1H-15N multiple quantum NMR." Biochemistry 28(9);4105-8. PMID: 2752012

Delihas75: Delihas N, Dunn JJ, Erdmann VA (1975). "The reaction of 5S RNA in 70S ribosomes with kethoxal." FEBS Lett 58(1);76-80. PMID: 773691

Delihas82: Delihas N, Andersen J (1982). "Generalized structures of the 5S ribosomal RNAs." Nucleic Acids Res 10(22);7323-44. PMID: 7155895

Digweed81: Digweed M, Erdmann VA, Odom OW, Hardesty B (1981). "Fluorescence modification of Escherichia coli 5S RNA." Nucleic Acids Res 9(13);3187-98. PMID: 6169004

Doctor72: Doctor BP, Brenner DJ (1972). "Isolation of 5S ribonucleic acid cistrons and tRNA cistrons from Escherichia coli." Biochem Biophys Res Commun 46(2);449-56. PMID: 4550693

Dohme76: Dohme F, Nierhaus KH (1976). "Role of 5S RNA in assembly and function of the 50S subunit from Escherichia coli." Proc Natl Acad Sci U S A 73(7);2221-5. PMID: 781671

Dontsova90: Dontsova OA, Efimov AV, Kopylov AM (1990). "[The 5S rRNA-protein complex of Escherichia coli studied by carbodiimide modification]." Nauchnye Doki Vyss Shkoly Biol Nauki (2);22-30. PMID: 1693861

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Doolittle70: Doolittle WF, Pace NR (1970). "Synthesis of 5S ribosomal RNA in Escherichia coli after rifampicin treatment." Nature 228(267);125-9. PMID: 4918254

Douthwaite79: Douthwaite S, Garrett RA, Wagner R, Feunteun J (1979). "A ribonuclease-resistant region of 5S RNA and its relation to the RNA binding sites of proteins L18 and L25." Nucleic Acids Res 6(7);2453-70. PMID: 379819

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Douthwaite82: Douthwaite S, Christensen A, Garrett RA (1982). "Binding site of ribosomal proteins on prokaryotic 5S ribonucleic acids: a study with ribonucleases." Biochemistry 21(10);2313-20. PMID: 6178424

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Feunteun70: Feunteun J, Jordan BR, Monier R (1970). "[Characterization of RNA 5S accumulated by a strain of Escherichia coli (RC relaxed) deficient in amino acids]." Bull Soc Chim Biol (Paris) 5(8);979-82. PMID: 4924729

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Forget70: Forget BG, Reynier M (1970). "Resistance of E. coli ribosomal 5S RNA to degradation by ribonuclease in reconstituted ribosomal particles." Biochem Biophys Res Commun 39(1);114-22. PMID: 4908845

Forget70a: Forget BG, Jordan B (1970). "5S RNA synthesized by Escherichia coli in presence of chloramphenicol: different 5'-terminal sequences." Science 167(917);382-4. PMID: 4902681

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Fox82: Fox JW, Wong KP (1982). "Acquisition of native conformation of ribosomal 5S ribonucleic acid from Escherichia coli. Hydrodynamic and spectroscopic studies on the unfolding and refolding of ribonucleic acid." Biochemistry 21(9);2096-102. PMID: 6807343

Fraser75: Fraser RS, Creanor J (1975). "The mechanism of inhibition of ribonucleic acid synthesis by 8-hydroxyquinoline and the antibiotic lomofungin." Biochem J 147(3);401-10. PMID: 810137

Galibert69: Galibert F, Sanfourche F (1969). "[Demonstration in sedimentation supernatant of ribosomes of a precursor 5S RNA pool]." C R Acad Sci Hebd Seances Acad Sci D 269(8);851-3. PMID: 4981108

Galibert71: Galibert F, Tiollais P, Sanfourche F, Boiron M (1971). "[Coordination of transcription of RNA 5 S and 23S and coordination of maturation of RNA 5S and of the ribosomal subunit 50S of Escherichia coli]." Eur J Biochem 20(3);381-91. PMID: 4931952

Garrett74: Garrett RA, Schulte C, Stoffler G, Gray P, Monier R (1974). "The release of proteins and 5S RNA during the unfolding of Escherichia coli ribosomes." FEBS Lett 49(1);1-4. PMID: 4216514

Garrett79: Garrett RA, Noller HF (1979). "Structures of complexes of 5S RNA with ribosomal proteins L5, L18 and L25 from Escherichia coli: identification of kethoxal-reactive sites on the 5S RNA." J Mol Biol 132(4);637-48. PMID: 393829

Georgellis92: Georgellis D, Arvidson S, von Gabain A (1992). "Decay of ompA mRNA and processing of 9S RNA are immediately affected by shifts in growth rate, but in opposite manners." J Bacteriol 174(16);5382-90. PMID: 1644765

Gewirth87: Gewirth DT, Abo SR, Leontis NB, Moore PB (1987). "Secondary structure of 5S RNA: NMR experiments on RNA molecules partially labeled with nitrogen-15." Biochemistry 26(16);5213-20. PMID: 2444255

Gewirth87a: Gewirth DT, Moore PB (1987). "Effects of mutation on the downfield proton nuclear magnetic resonance spectrum of the 5S RNA of Escherichia coli." Biochemistry 26(18);5657-65. PMID: 3314994

Gewirth88: Gewirth DT, Moore PB (1988). "Exploration of the L18 binding site on 5S RNA by deletion mutagenesis." Nucleic Acids Res 16(22);10717-32. PMID: 3060848

Ghora78: Ghora BK, Apirion D (1978). "Structural analysis and in vitro processing to p5 rRNA of a 9S RNA molecule isolated from an rne mutant of E. coli." Cell 15(3);1055-66. PMID: 365352

Ghora79: Ghora BK, Apirion D (1979). "5S ribosomal RNA is contained within a 25 S ribosomal RNA that accumulates in mutants of Escherichia coli defective in processing of ribosomal RNA." J Mol Biol 127(4);507-13. PMID: 372546

Glotz81: Glotz C, Zwieb C, Brimacombe R, Edwards K, Kossel H (1981). "Secondary structure of the large subunit ribosomal RNA from Escherichia coli, Zea mays chloroplast, and human and mouse mitochondrial ribosomes." Nucleic Acids Res 9(14);3287-306. PMID: 7024913

Goldblum81: Goldblum K, Apririon D (1981). "Inactivation of the ribonucleic acid-processing enzyme ribonuclease E blocks cell division." J Bacteriol 146(1);128-32. PMID: 6163761

Gorelic78: Gorelic L, Parker D (1978). "Studies of the effects of ultraviolet radiation on the structural integrities of ribosomal RNA components of the Escherichia coli 50S ribosomal subunit." Biochemistry 17(15);3152-62. PMID: 359042

Goringer84: Goringer HU, Szymkowiak C, Wagner R (1984). "Escherichia coli 5S RNA A and B conformers. Characterisation by enzymatic and chemical methods." Eur J Biochem 144(1);25-34. PMID: 6207022

Goringer84a: Goringer HU, Wagner R, Jacob WF, Dahlberg AE, Zwieb C (1984). "Oligonucleotide directed mutagenesis of Escherichia coli 5S ribosomal RNA: construction of mutant and structural analysis." Nucleic Acids Res 12(18);6935-50. PMID: 6091046

Goringer86: Goringer HU, Wagner R (1986). "Does 5S RNA from E. coli have a pseudoknotted structure?." Nucleic Acids Res 14(18);7473-85. PMID: 2429262

Goringer86a: Goringer HU, Wagner R (1986). "Construction and functional analysis of ribosomal 5S RNA from Escherichia coli with single base changes in the ribosomal protein binding sites." Biol Chem Hoppe Seyler 367(8);769-80. PMID: 2429677

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Gray72: Gray PN, Monier R (1972). "Partial localization of the 5S RNA binding site on 23S RNA." Biochimie 54(1);41-5. PMID: 4568456

Grune96: Grune M, Gorlach M, Soskic V, Klussmann S, Bald R, Furste JP, Erdmann VA, Brown LR (1996). "Initial analysis of 750 MHz NMR spectra of selective 15N-G,U labelled E. coli 5S rRNA." FEBS Lett 385(1-2);114-8. PMID: 8641454

Grune96a: Grune M, Furste JP, Klussmann S, Erdmann VA, Brown LR (1996). "Detection of multiple conformations of the E-domain of 5S rRNA from Escherichia coli in solution and in crystals by NMR spectroscopy." Nucleic Acids Res 24(13);2592-6. PMID: 8692701

Hancock82: Hancock J, Wagner R (1982). "A structural model of 5S RNA from E. coli based on intramolecular crosslinking evidence." Nucleic Acids Res 10(4);1257-69. PMID: 7041089

Hernandez75: Hernandez F, Vazquez D, Ballesta JP (1975). "Partial reconstitution of active ribosomes and 50S subunits." Biochemistry 14(7);1503. PMID: 164889

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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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