RegulonDB RegulonDB 11.1: Gene Form

rrlC gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

rrlC rrfC gltU trpTp2 trpTp2 aspTp1 aspTp1

Name: rrlC    Texpresso search in the literature
Synonym(s): ECK3752, EG30079, b3758
Genome position(nucleotides): 3943704 --> 3946607
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
External database links:  

Name: 23S ribosomal RNA
Synonym(s): 23S rRNA, rrlC, rrlC 23S ribosomal RNA
Type: rRNA
Cellular location: cytosol
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.6 - rRNA, stable RNA
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0022625 - cytosolic large ribosomal subunit
biological_process GO:0006412 - translation
Note(s): Note(s): ...[more].
Evidence: [EXP-TAS] Traceable author statement to experimental support
Reference(s): [1] Apirion D., et al., 1976
[2] Arkov AL., et al., 1998
[3] Asai T., et al., 1999
[4] Babkina GT., et al., 1988
[5] Banatao DR., et al., 2003
[6] Bayfield MA., et al., 2001
[7] Bessarab DA., et al., 1998
[8] Boddeker N., et al., 1997
[9] Bukhman YV., et al., 1997
[10] Chattopadhyay S., et al., 1996
[11] Chattopadhyay S., et al., 1999
[12] Chernyaeva NS., et al., 1999
[13] Chui HM., et al., 2002
[14] Chui HM., et al., 2002
[15] Cooperman BS., et al., 1995
[16] Das B., et al., 1996
[17] Dennis PP., et al., 1976
[18] Diges CM., et al., 2001
[19] Dontsova O., et al., 1994
[20] Endo Y., et al., 1988
[21] Frank J., et al., 1991
[22] Fuchs BM., et al., 2001
[23] Fuller-Pace FV., et al., 1993
[24] Gimautdinova OI., et al., 1982
[25] Gorelic L., et al., 1978
[26] Guerin MF., et al., 1983
[27] Habuka N., et al., 1991
[28] Harrod R., et al., 1995
[29] Hellman U., et al., 1980
[30] Horie K., et al., 1983
[31] Horie K., et al., 1981
[32] Hui Bon Hoa G., et al., 1977
[33] Jones DS., et al., 1976
[34] Kakegawa T., et al., 1986
[35] Karpova GG., et al., null
[36] Kliber JS., et al., 1976
[37] Kudlicki W., et al., 1997
[38] Littlechild J. 1973
[39] Mandiyan V., et al., 1990
[40] Markey F., et al., 1976
[41] Mawn MV., et al., 2002
[42] Meyer HA., et al., 1996
[43] Misra VK., et al., 2001
[44] Misra VK., et al., 2002
[45] Mohanty BK., et al., 2000
[46] Morris DR., et al., 1974
[47] Morris DR., et al., 1975
[48] Muth GW., et al., 2001
[49] Nicol SM., et al., 1995
[50] Nisen P., et al., null
[51] Noskov VA. 1972
[52] Odom OW., et al., 1980
[53] Pal D., et al., 1997
[54] Polacek N., et al., 1998
[55] Polach KJ., et al., 2002
[56] Pugh GE., et al., 1999
[57] Rinke-Appel J., et al., 2002
[58] Sanyal SC., et al., 2002
[59] Schindler DG., et al., 1977
[60] Schwartz I., et al., 1975
[61] Semrad K., et al., 2002
[62] Shiman R., et al., 2000
[63] Siehnel RJ., et al., 1985
[64] Spahn CM., et al., 2000
[65] Sykes J., et al., 1977
[66] Sykes J., et al., 1977
[67] Takeda E., et al., 1997
[68] Tenson T., et al., 1996
[69] Tewari DS., et al., 1983
[70] Thomas GJ., et al., 1980
[71] Thompson J., et al., 1993
[72] Tsu CA., et al., 2001
[73] Tsu CA., et al., 1998
[74] Welch M., et al., 1995
[75] White GA., et al., 1988
[76] Wower J., et al., 1994
[77] Yamagishi M., et al., 1988
[78] Yates JL., et al., 1981
[79] Yi QM., et al., 1982
[80] Yu MT., et al., 1970
[81] Yuan D., et al., 1975
External database links:  

Name: rrsC-gltU-rrlC-rrfC         
Operon arrangement:
Transcription unit        Promoter

Transcriptional Regulation      
Display Regulation             
Activated by: Fis
Repressed by: H-NS, Lrp

Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter aspTp1 3946780 forward nd [COMP-AINF] [82]
  promoter trpTp2 3946780 forward nd [COMP-AINF] [82]


 [COMP-AINF] Inferred computationally without human oversight


 [1] Apirion D., Neil J., Watson N., 1976, Consequences of losing ribonuclease III on the Escherichia coli cell., Mol Gen Genet 144(2):185-90

 [2] Arkov AL., Mankin A., Murgola EJ., 1998, An rRNA fragment and its antisense can alter decoding of genetic information., J Bacteriol 180(10):2744-8

 [3] Asai T., Zaporojets D., Squires C., Squires CL., 1999, An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria., Proc Natl Acad Sci U S A 96(5):1971-6

 [4] Babkina GT., Vladimirov SN., Karpova GG., 1988, [Affinity modification of Escherichia coli ribosomes with the non-hydrolyzed GTP analog, gamma-[4-N-(2-chloroethyl)-N-methylaminobenzyl]amide of GTP], Bioorg Khim 14(4):472-7

 [5] Banatao DR., Altman RB., Klein TE., 2003, Microenvironment analysis and identification of magnesium binding sites in RNA., Nucleic Acids Res 31(15):4450-60

 [6] Bayfield MA., Dahlberg AE., Schulmeister U., Dorner S., Barta A., 2001, A conformational change in the ribosomal peptidyl transferase center upon active/inactive transition., Proc Natl Acad Sci U S A 98(18):10096-101

 [7] Bessarab DA., Kaberdin VR., Wei CL., Liou GG., Lin-Chao S., 1998, RNA components of Escherichia coli degradosome: evidence for rRNA decay., Proc Natl Acad Sci U S A 95(6):3157-61

 [8] Boddeker N., Stade K., Franceschi F., 1997, Characterization of DbpA, an Escherichia coli DEAD box protein with ATP independent RNA unwinding activity., Nucleic Acids Res 25(3):537-45

 [9] Bukhman YV., Draper DE., 1997, Affinities and selectivities of divalent cation binding sites within an RNA tertiary structure., J Mol Biol 273(5):1020-31

 [10] Chattopadhyay S., Das B., Dasgupta C., 1996, Reactivation of denatured proteins by 23S ribosomal RNA: role of domain V., Proc Natl Acad Sci U S A 93(16):8284-7

 [11] Chattopadhyay S., Pal S., Pal D., Sarkar D., Chandra S., Das Gupta C., 1999, Protein folding in Escherichia coli: role of 23S ribosomal RNA., Biochim Biophys Acta 1429(2):293-8

 [12] Chernyaeva NS., Murgola EJ., Mankin AS., 1999, Suppression of nonsense mutations induced by expression of an RNA complementary to a conserved segment of 23S rRNA., J Bacteriol 181(17):5257-62

 [13] Chui HM., Desaulniers JP., Scaringe SA., Chow CS., 2002, Synthesis of helix 69 of Escherichia coli 23S rRNA containing its natural modified nucleosides, m(3)Psi and Psi., J Org Chem 67(25):8847-54

 [14] Chui HM., Meroueh M., Scaringe SA., Chow CS., 2002, Synthesis of a 3-methyluridine phosphoramidite to investigate the role of methylation in a ribosomal RNA hairpin., Bioorg Med Chem 10(2):325-32

 [15] Cooperman BS., Alexander RW., Muralikrishna P., 1995, Photolabile oligoDNA probes of internal Escherichia coli ribosomal structure., Nucleic Acids Symp Ser NIL(33):59-62

 [16] Das B., Chattopadhyay S., Bera AK., Dasgupta C., 1996, In vitro protein folding by ribosomes from Escherichia coli, wheat germ and rat liver: the role of the 50S particle and its 23S rRNA., Eur J Biochem 235(3):613-21

 [17] Dennis PP., Nordan DH., 1976, Characterization of the hybridization between purified 16S and 23S ribosomal ribonucleic acid and ribosomal deoxyribonucleic acid from Escherichia coli., J Bacteriol 128(1):28-34

 [18] Diges CM., Uhlenbeck OC., 2001, Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA., EMBO J 20(19):5503-12

 [19] Dontsova O., Tishkov V., Dokudovskaya S., Bogdanov A., Doring T., Rinke-Appel J., Thamm S., Greuer B., Brimacombe R., 1994, Stem-loop IV of 5S rRNA lies close to the peptidyltransferase center., Proc Natl Acad Sci U S A 91(10):4125-9

 [20] Endo Y., Tsurugi K., 1988, The RNA N-glycosidase activity of ricin A-chain., Nucleic Acids Symp Ser (19):139-42

 [21] Frank J., Penczek P., Grassucci R., Srivastava S., 1991, Three-dimensional reconstruction of the 70S Escherichia coli ribosome in ice: the distribution of ribosomal RNA., J Cell Biol 115(3):597-605

 [22] Fuchs BM., Syutsubo K., Ludwig W., Amann R., 2001, In situ accessibility of Escherichia coli 23S rRNA to fluorescently labeled oligonucleotide probes., Appl Environ Microbiol 67(2):961-8

 [23] Fuller-Pace FV., Nicol SM., Reid AD., Lane DP., 1993, DbpA: a DEAD box protein specifically activated by 23s rRNA., EMBO J 12(9):3619-26

 [24] Gimautdinova OI., Karpova GG., Kozyreva NA., 1982, [Affinity labeling of ribosomes from Escherichia coli with 4-(N-2-chloroethyl-N-methylamino) benzyl-5'-phosphamides of oligouridylates of different length]., Mol Biol (Mosk) 16(4):752-62

 [25] 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

 [26] Guerin MF., Hayes D., 1983, Concerning the thermal stability of E. coli 23S ribosomal RNA., Biochimie 65(6):345-54

 [27] Habuka N., Miyano M., Kataoka J., Noma M., 1991, Escherichia coli ribosome is inactivated by Mirabilis antiviral protein which cleaves the N-glycosidic bond at A2660 of 23 S ribosomal RNA., J Mol Biol 221(3):737-43

 [28] Harrod R., Lovett PS., 1995, Peptide inhibitors of peptidyltransferase alter the conformation of domains IV and V of large subunit rRNA: a model for nascent peptide control of translation., Proc Natl Acad Sci U S A 92(19):8650-4

 [29] Hellman U., Svensson I., 1980, Preparative scale fractionation of Escherichai coli robosomal RNA and transfer RNA on Sjepharose 6B., Prep Biochem 10(4):375-86

 [30] Horie K., Hagihara H., Wada A., Fukutome H., 1983, Magnesium ion induced proton release as a probe for the polyelectrolytic structure of ribosomal RNAs and subunits., J Biochem (Tokyo) 94(4):1289-99

 [31] Horie K., Wada A., Fukutome H., 1981, Conformational studies of Escherichia coli ribosomes with the use of acridine orange as a probe., J Biochem (Tokyo) 90(2):449-61

 [32] Hui Bon Hoa G., Graffe M., Grunberg-Manago M., 1977, Thermodynamic studies of the reversible association of Escherichia coli ribosomal subunits., Biochemistry 16(12):2800-5

 [33] Jones DS., Lundgren HK., Jay FT., 1976, The separation of ribonucleic acids from Escherichia coli on lysin-agarose., Nucleic Acids Res 3(6):1569-76

 [34] Kakegawa T., Hirose S., Kashiwagi K., Igarashi K., 1986, Effect of polyamines on in vitro reconstitution of ribosomal subunits., Eur J Biochem 158(2):265-9

 [35] Karpova GG., Pichko NP., Chimitova TA., Grineva NI., null, [Complementarily addressed alkylation of Escherichia coli ribosomal RNA in complexes with particular conformation], Mol Biol (Mosk) 13(5):1012-20

 [36] Kliber JS., Hoa GH., Douzou P., Graffe M., Grunberg-Manago M., 1976, Implications of electrostatic potentials on ribosomal proteins., Nucleic Acids Res 3(12):3423-38

 [37] Kudlicki W., Coffman A., Kramer G., Hardesty B., 1997, Ribosomes and ribosomal RNA as chaperones for folding of proteins., Fold Des 2(2):101-8

 [38] Littlechild J., 1973, Nuclease contaminant of a batch of lysozyme used for ribosome extraction: cleavage of Escherichia coli 23S rRNA into two specific fragments., Anal Biochem 55(2):634-6

 [39] Mandiyan V., Tumminia S., Wall JS., Boublik M., 1990, Visualization of ion-dependent conformational changes in Escherichia coli 23 S rRNA by scanning transmission electron microscopy., Arch Biochem Biophys 276(2):299-304

 [40] Markey F., Sims PF., Wild DG., 1976, The composition of an unusual precursor of 50 S ribosomes in a mutant of Escherichia coli., Biochem J 158(2):451-6

 [41] Mawn MV., Fournier MJ., Tirrell DA., Mason TL., 2002, Depletion of free 30S ribosomal subunits in Escherichia coli by expression of RNA containing Shine-Dalgarno-like sequences., J Bacteriol 184(2):494-502

 [42] Meyer HA., Triana-Alonso F., Spahn CM., Twardowski T., Sobkiewicz A., Nierhaus KH., 1996, Effects of antisense DNA against the alpha-sarcin stem-loop structure of the ribosomal 23S rRNA., Nucleic Acids Res 24(20):3996-4002

 [43] Misra VK., Draper DE., 2001, A thermodynamic framework for Mg2+ binding to RNA., Proc Natl Acad Sci U S A 98(22):12456-61

 [44] Misra VK., Draper DE., 2002, The linkage between magnesium binding and RNA folding., J Mol Biol 317(4):507-21

 [45] Mohanty BK., Kushner SR., 2000, Polynucleotide phosphorylase, RNase II and RNase E play different roles in the in vivo modulation of polyadenylation in Escherichia coli., Mol Microbiol 36(4):982-94

 [46] Morris DR., Dahlberg JE., Dahlberg AE., 1974, Detection of cation-specific conformational changes in ribosomal RNA by gel electrophoresis., Nucleic Acids Res 1(10):1249-58

 [47] Morris DR., Dahlberg JE., Dahlberg AE., 1975, Detection of cation-specific conformational changes in ribosomal RNA by gel electrophoresis., Nucleic Acids Res 2(4):447-58

 [48] Muth GW., Chen L., Kosek AB., Strobel SA., 2001, pH-dependent conformational flexibility within the ribosomal peptidyl transferase center., RNA 7(10):1403-15

 [49] Nicol SM., Fuller-Pace FV., 1995, The "DEAD box" protein DbpA interacts specifically with the peptidyltransferase center in 23S rRNA., Proc Natl Acad Sci U S A 92(25):11681-5

 [50] Nisen P., Shapiro L., null, E. coli ribosomal RNA contains sequences homologous to insertion sequences IS1 and IS2., Nature 282(5741):872-4

 [51] Noskov VA., 1972, [Frequency of occurrence of purine isoplites in 16S- and 23S-ribosomal RNA of Escherichia coli MRE-600], Dokl Akad Nauk SSSR 205(5):1246-7

 [52] Odom OW., Robbins DJ., Lynch J., Dottavio-Martin D., Kramer G., Hardesty B., 1980, Distances between 3' ends of ribosomal ribonucleic acids reassembled into Escherichia coli ribosomes., Biochemistry 19(26):5947-54

 [53] Pal D., Chattopadhyay S., Chandra S., Sarkar D., Chakraborty A., Das Gupta C., 1997, Reactivation of denatured proteins by domain V of bacterial 23S rRNA., Nucleic Acids Res 25(24):5047-51

 [54] Polacek N., Barta A., 1998, Metal ion probing of rRNAs: evidence for evolutionarily conserved divalent cation binding pockets., RNA 4(10):1282-94

 [55] Polach KJ., Uhlenbeck OC., 2002, Cooperative binding of ATP and RNA substrates to the DEAD/H protein DbpA., Biochemistry 41(11):3693-702

 [56] Pugh GE., Nicol SM., Fuller-Pace FV., 1999, Interaction of the Escherichia coli DEAD box protein DbpA with 23 S ribosomal RNA., J Mol Biol 292(4):771-8

 [57] Rinke-Appel J., Osswald M., von Knoblauch K., Mueller F., Brimacombe R., Sergiev P., Avdeeva O., Bogdanov A., Dontsova O., 2002, Crosslinking of 4.5S RNA to the Escherichia coli ribosome in the presence or absence of the protein Ffh., RNA 8(5):612-25

 [58] Sanyal SC., Pal S., Chowdhury S., DasGupta C., Chaudhuri S., 2002, 23S rRNA assisted folding of cytoplasmic malate dehydrogenase is distinctly different from its self-folding., Nucleic Acids Res 30(11):2390-7

 [59] Schindler DG., Davies JE., 1977, Specific cleavage of ribosomal RNA caused by alpha sarcin., Nucleic Acids Res 4(4):1097-1110

 [60] Schwartz I., Gordon E., Ofengand J., 1975, Photoaffinity labeling of the ribosomal A site with S-(p-azidophenacyl)valyl-tRNA., Biochemistry 14(13):2907-14

 [61] Semrad K., Green R., 2002, Osmolytes stimulate the reconstitution of functional 50S ribosomes from in vitro transcripts of Escherichia coli 23S rRNA., RNA 8(4):401-11

 [62] Shiman R., Draper DE., 2000, Stabilization of RNA tertiary structure by monovalent cations., J Mol Biol 302(1):79-91

 [63] Siehnel RJ., Morgan EA., 1985, Unbalanced rRNA gene dosage and its effects on rRNA and ribosomal-protein synthesis., J Bacteriol 163(2):476-86

 [64] Spahn CM., Penczek PA., Leith A., Frank J., 2000, A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome., Structure Fold Des 8(9):937-48

 [65] Sykes J., Metcalf E., Pickering JD., 1977, The nature of the proteins in 'chloramphenicol particles' from Escherichia coli A19 (Hfr rel met rns)., J Gen Microbiol 98(1):1-16

 [66] Sykes J., Metcalf E., Pickering JD., 1977, The nature of the proteins present in the 'relaxed particles' from methionine-starved Escherichia coli A19 (Hfr rel met rns)., J Gen Microbiol 98(1):17-27

 [67] Takeda E., Bi X., Yoshinari S., Endo Y., 1997, Mechanism of substrate recognition by the ribotoxin, alpha-sarcin., Nucleic Acids Symp Ser (37):131-2

 [68] Tenson T., DeBlasio A., Mankin A., 1996, A functional peptide encoded in the Escherichia coli 23S rRNA., Proc Natl Acad Sci U S A 93(11):5641-6

 [69] Tewari DS., Burma DP., 1983, Incorporation of 5S RNA into 16S-23S RNA complex., Biochem Biophys Res Commun 114(1):348-54

 [70] Thomas GJ., Prescott B., Hamilton MG., 1980, Raman spectra and conformational properties of ribosomes during various stages of disassembly., Biochemistry 19(15):3604-13

 [71] Thompson J., Musters W., Cundliffe E., Dahlberg AE., 1993, Replacement of the L11 binding region within E.coli 23S ribosomal RNA with its homologue from yeast: in vivo and in vitro analysis of hybrid ribosomes altered in the GTPase centre., EMBO J 12(4):1499-504

 [72] Tsu CA., Kossen K., Uhlenbeck OC., 2001, The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA., RNA 7(5):702-9

 [73] Tsu CA., Uhlenbeck OC., 1998, Kinetic analysis of the RNA-dependent adenosinetriphosphatase activity of DbpA, an Escherichia coli DEAD protein specific for 23S ribosomal RNA., Biochemistry 37(48):16989-96

 [74] Welch M., Chastang J., Yarus M., 1995, An inhibitor of ribosomal peptidyl transferase using transition-state analogy., Biochemistry 34(2):385-90

 [75] White GA., Wood T., Hill WE., 1988, Probing the alpha-sarcin region of Escherichia coli 23S rRNA with a cDNA oligomer., Nucleic Acids Res 16(22):10817-31

 [76] Wower J., Hixson SS., Sylvers LA., Xing Y., Zimmermann RA., 1994, Synthesis of 2,6-diazido-9-(beta-D-ribofuranosyl)purine 3',5'-bisphosphate: incorporation into transfer RNA and photochemical labeling of Escherichia coli ribosomes., Bioconjug Chem 5(2):158-61

 [77] Yamagishi M., Nomura M., 1988, Effects of induction of rRNA overproduction on ribosomal protein synthesis and ribosome subunit assembly in Escherichia coli., J Bacteriol 170(11):5042-50

 [78] Yates JL., Nomura M., 1981, Feedback regulation of ribosomal protein synthesis in E. coli: localization of the mRNA target sites for repressor action of ribosomal protein L1., Cell 24(1):243-9

 [79] Yi QM., Wong KP., 1982, The effects of magnesium ions on the hydrodynamic shape, conformation, and stability of the ribosomal 23S RNA from E. coli., Biochem Biophys Res Commun 104(2):733-9

 [80] Yu MT., Vermeulen CW., Atwood KC., 1970, Location of the genes for 16S and 23S ribosomal RNA in the genetic map of Escherichia coli., Proc Natl Acad Sci U S A 67(1):26-31

 [81] Yuan D., Shen V., 1975, Stability of ribosomal and transfer ribonucleic acid in Escherichia coli B/r after treatment with ethylenedinitrilotetraacetic acid and rifampicin., J Bacteriol 122(2):425-32

 [82] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78