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Escherichia coli K-12 substr. MG1655 RNA: rrlE 23S ribosomal RNA



Gene: rrlE Accession Numbers: EG30081 (EcoCyc), b4009, ECK4001

Superclasses: 23S rRNA

Regulation Summary Diagram: ?

Summary:
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 [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 23S rRNA has been described [Nichols67, Cramer68, Fellner68, Woese68, Schaup69, Fellner69, Fellner70, Fellner71, Branlant75, Herr75, Branlant76, Branlant77, Herr78, Zwieb78, Sloof78, Krol78, Sri79, Edlind80, Brosius80, Branlant81, Machatt81, Jacq81, Glotz81, Branlant81a, Noller81, Stiege82, Stiege83, Turner83, Maly83, Klein85, Gongadze, Egebjerg87, Marconi88, Nagano88, Hausner88, Leffers88, Haselman89, Mitchell90, Brimacombe90, Muralikrishna91, Doring91, Aagaard91, Agrawal92, Leviev94, Aagaard94, Rosendahl95, Mueller95a, OConnor96, Liiv98, Baranov98, Leontis98, Muth99, Dorner99, Correll99, Spahn99, Chernyaeva00, Gutell00, Blanchard01, Matadeen01, Elgavish01, Klein01, Winkler01, Kubarenko01, Correll03].

The relationship of the 23S rRNA to ribosome assembly, structure, and function has been characterized [Sonenberg75, Dahlberg78, Schreiber79, Gray72, Newberry80, StofflerMeilick81, Rohl82, Chiam83, Skold83, Burma83, Barta83, Barta84, Meier85, Skinner85, Hall85, Hausner87, Babkina88, Moazed88, Steiner88, Thanaraj88, Leffers88, Marconi89, Thanaraj89, Moazed89, Wower89, Tapprich90, Hill90, Wollenzien91, Podkowinski91, Moazed91, Ryan91, Tapio91, Mitchell92, Noller92, Bhangu92, Melancon92, Brimacombe93, Mitchell93, OConnor93a, Rosendahl93, Stade94, Lieberman94, Muralikrishna95, Stade95, Samaha95, Bullard95, Osswald95, RinkeAppel95, OConnor95, Joseph96, Porse96, Spahn96, Saarma97, Munishkin97, Zvereva98, Choi98, Arkov98, Green98, Bocchetta98, Sergiev98, Ostergaard98, Merryman99, Culver99, Osswald99, Holmberg99, Cheung, Culver99a, Bukhtiyarov99, Kim99, Vladimirov00, Mueller00, Lieberman00, Koosha00, Polacek00, Wower00, Polacek01, Thompson01, La01, Feinberg01, Xu02, Kirillov02, Van02, Katunin02, Arkov02, Polacek02, Stark02, Polacek03, Beringer03].

Interactions between the 23S rRNA and ribosomal proteins have been described [Stoffler72, Schulte74, Spiridonova, Schulte75, Sloof76, Spierer76, Tritton76, Branlant76a, Spierer79, Pettersson79, Dijk79, Marquardt79, Giocanti80, Maly80, Branlant80, Skold81, Wower81, Rohl82a, Gulle88, Chistyakov88, Beauclerk88, Said88, Chistyakov89, Ryan89, Egebjerg90, Osswald90, Zengel91, Brimacombe91, Karaoglu91, Ryan91a, Egebjerg91, Zengel93, Rosendahl93, Murgola95, Urlaub95, Adamski96, Thiede98, Kohrer98, Uchiumi99, Lieberman98, Blyn00, Stelzl00, Stelzl00a, Drygin00, Stelzl01, Todorova03].

Analysis of mutations in 23S rRNA has been conducted [Zweib84, Sirdeshmukh85a, Nishi86, Thompson88, Vester88, Said88, Tapprich90, Tapio91, Douthwaite92, Vannuffel92, Saarma92, Melancon92, Douthwaite93, OConnor93a, Bilgin94, Gregory94, Rosendahl94, Aagaard94, Lieberman94, Marchant94, Murgola95, Leviev95, Porse95, Rosendahl95, Rosendahl95a, Murgola95a, OConnor95, Jemiolo95, Triman96, OConnor96, Liiv96, Xu96, Porse96, Spahn96a, Triman97, Green97, Saarma97, Munishkin97, Zvereva98, Triman98, Arkov98, Liiv98, Saarma98, Gregory99, Macbeth99, Asai99, Raychaudhuri99, Triman99, Kim99, Chan00, Sergiev00, Muth00, Koosha00, Chernyaeva00, OConnor01, Polacek01, Thompson01, Maivali, GarzaRamos01, Xu02, Brunelli02, Katunin02, Arkov02, Polacek02, Polacek03, Leonov03, Kim01, Beringer03].

The relationship of the 23S rRNA to sensitivity to multiple antibiotics is discussed [Hogenauer81, Cundliffe81, Sigmund82, Sigmund84, Ettayebi85, Douthwaite85, Vester87, Moazed87, Arthur87, Sigmund88, Hall88, BrissonNoel88, Thompson88, Vester88, Egebjerg89, Douthwaite89, Marconi90, Miller91a, Thompson, Egebjerg, Ryan91a, Douthwaite92, Vannuffel92, Saarma92, Douthwaite92a, Douthwaite93, Rosendahl93, Bilgin94, Rosendahl94, Leviev94, RodriguezFonsec95, Douthwalte95, Tenson96, Dam96, Oehler97, Hansen99, Xiong99, Dorner99, Porse99, Gregory99a, Matassova99, Porse99a, Kirillov99, Rodnina99, Blyn00, Douthwaite00, RodriguezFonsec00, Xiong00, Poulsen00, Usary01, Poulsen01, GarzaRamos01, Nakajima99, Aoki02, Hansen02, Kofoed02, Dinos03, Bobkova03].

The 23S rRNA encodes a short peptide that plays a role in erythromycin resistance [Tenson95, Tenson96, Dam96].

The 23S rRNA is subject to pseudouridylation, dihydrouridylation, and methylation. Processing and modification of the 23S rRNA has been characterized [Branlant75, Duncan75, Pardo77, Hofmann77, Andersen78, Bjork78, Apirion78a, Pardo79, Lebenka, Bram80, Gegenheimer80, King84, Clark84, Sirdeshmukh85, ThakkerVaria85, Szymkowiak88, Srivastava88, Weitzmann90, Smith92, Bakin93, Wrzesinski95, Vester95, Kowalak95, Zhong95, Kowalak96, Dalluge96, Green96, Gustafsson98, Conrad98, Raychaudhuri98, Huang98, Hansen99a, Li99a, Villsen99, Corollo99, Nielsen99a, Meroueh00, Caldas00, Charette00, Bugl00, Wrzesinski00, OConnor01, Gutgsell01, Hansen01a, Lovgren01, Del01, Agarwalla02, Tan02, Michel02, Allas03, Madsen03, Andersen04].

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

Reviews [Arthur87, BrissonNoel88, Dahlberg89, Srivastava91, Brimacombe91, Brimacombe92, Lane92, Mueller95a, Wower95, Tenson95, Liebman95, Douthwalte95, Triman96, Triman97, Triman98, Triman99, Charette00, Nakajima99, Stark02a, Kim01].

Citations: [Galibert71, Bremer71, Kossman71, Muto75, Lindahl75, Reiness75, Shinnick75, Lund76, Yamamoto76, Muto77, Muto77a, Vola77, Morgan77, Chaney77, Morgan78, Jorgensen78, Sekiya80, Ellwood82, Steen86, Zacharias87, Szymkowiak87, Harvey88, Zacharias89, Theissen90, Theissen90a, Lewicki93, Kalpaxis95, Heinrich95, Pfeiffer97, Kalpaxis98, Hashimoto03, Yu70, Noskov72, Littlechild73, Morris75, Yuan75, Schwartz75, Apirion76a, Jones76, Markey76, Dennis76, Kliber76, Sykes77, Sykes77a, Schindler77, Hui77, Gorelic78, Karpova, Nisen, Hellman80, Thomas80, Odom80, Yates81, Horie81, Yi82, Gimautdinova, Guerin83, Tewari83, Horie83, Siehnel85, Kakegawa86, Endo88, Babkina88a, Yamagishi88, White88, Mandiyan90, Habuka91, Frank91, Thompson93, FullerPace93, Wower, Dontsova94, Cooperman95, Welch95, Harrod95, Nicol95, Das96, Chattopadhyay96, Meyer96, Kudlicki97, Boddeker97, Bukhman97, Pal97, Bessarab98, Takeda97, Arkov98a, Polacek98, Tsu98, Chattopadhyay99, Asai99a, Chernyaeva99, Pugh99, Morris74, Mohanty00, Shiman00, Spahn00, Fuchs01, Tsu01, Bayfield01, Diges01, Misra01, Muth01, Chui02, Mawn02, Polach02, Misra02, Semrad02, RinkeAppel02, Sanyal02, Chui02a, Banatao03]

Map Position: [4,208,066 -> 4,210,969] (90.7 centisomes)
Length: 2904 bp

Reactions known to consume the compound:

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


rRNA + S-adenosyl-L-methionine → rRNA containing N6,N6-dimethyladenine + S-adenosyl-L-homocysteine


23S rRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]

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
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]

Genetic Regulation Schematic: ?

Unification Links: ASAP:ABE-0013107 , CGSC:199 , EchoBASE:EB4244 , EcoGene:EG30081 , EcoliWiki:b4009 , OU-Microarray:b4009 , PortEco:rrlE , RegulonDB:EG30081

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): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4009 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG30081.


References

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Barta84: Barta A, Steiner G, Brosius J, Noller HF, Kuechler E (1984). "Identification of a site on 23S ribosomal RNA located at the peptidyl transferase center." Proc Natl Acad Sci U S A 81(12);3607-11. PMID: 6374660

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Other References Related to Gene Regulation

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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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