RegulonDB

Gene
Name:	rrlD
Synonym(s):	ECK3262, EG30080, b3275
Genome position(nucleotides):	3423880 <-- 3426783
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.34
External database links:

ASAP:	ABE-0010746
CGSC:	200
ECHOBASE:	EB4243
ECOLIHUB:	rrlD
OU-MICROARRAY:	b3275
COLOMBOS:	rrlD

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

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	rrfFp2	3423707		reverse	nd	[COMP-AINF]	[113]

Evidence
[COMP-AINF] Inferred computationally without human oversight

Reference(s)
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[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
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[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] Bremer H., Berry L., 1971, Co-transcription of 16S and 23S ribosomal RNA in Escherichia coli., Nat New Biol 234(46):81-3
[10] 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
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[12] 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
[13] 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
[14] 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
[15] 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
[16] 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
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[21] 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
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[33] Harvey S., Hill CW., Squires C., Squires CL., 1988, Loss of the spacer loop sequence from the rrnB operon in the Escherichia coli K-12 subline that bears the relA1 mutation., J Bacteriol 170(3):1235-8
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[36] 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
[37] 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
[38] 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
[39] 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
[40] 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
[41] Jorgensen P., Collins J., Fiil N., von Meyenbourg K., 1978, A ribosomal RNA gene, rrnC, of Escherichia coli, mapped by specialized transducing lambdadilv and lambda drbs phages., Mol Gen Genet 163(2):223-8
[42] 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
[43] Kalpaxis DL., Karahalios P., Papapetropoulou M., 1995, Growth phase and growth rate dependence of ribosomal peptidyltransferase activity status in Escherichia coli., Biochimie 77(12):963-71
[44] Kalpaxis DL., Karahalios P., Papapetropoulou M., 1998, Changes in ribosomal activity of Escherichia coli cells during prolonged culture in sea salts medium., J Bacteriol 180(12):3114-9
[45] 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
[46] 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
[47] Kossman CR., Stamato TD., Pettijohn DE., 1971, Tandem synthesis of the 16S and 23S ribosomal RNA sequences of Escherichia coli., Nat New Biol 234(47):102-4
[48] 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
[49] Lewicki BT., Margus T., Remme J., Nierhaus KH., 1993, Coupling of rRNA transcription and ribosomal assembly in vivo. Formation of active ribosomal subunits in Escherichia coli requires transcription of rRNA genes by host RNA polymerase which cannot be replaced by bacteriophage T7 RNA polymerase., J Mol Biol 231(3):581-93
[50] Lindahl L., Jaskunas SR., Dennis PP., Nomura M., 1975, Cluster of genes in Escherichia coli for ribosomal proteins, ribosomal RNA, and RNA polymerase subunits., Proc Natl Acad Sci U S A 72(7):2743-7
[51] 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
[52] Lund E., Dahlberg JE., Lindahl L., Jaskunas SR., Dennis PP., Nomura M., 1976, Transfer RNA genes between 16S and 23S rRNA genes in rRNA transcription units of E. coli., Cell 7(2):165-77
[53] 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
[54] 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
[55] 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
[56] 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
[57] Misra VK., Draper DE., 2001, A thermodynamic framework for Mg2+ binding to RNA., Proc Natl Acad Sci U S A 98(22):12456-61
[58] Misra VK., Draper DE., 2002, The linkage between magnesium binding and RNA folding., J Mol Biol 317(4):507-21
[59] 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
[60] Morgan EA., Ikemura T., Lindahl L., Fallon AM., Nomura M., 1978, Some rRNA operons in E. coli have tRNA genes at their distal ends., Cell 13(2):335-44
[61] Morgan EA., Ikemura T., Nomura M., 1977, Identification of spacer tRNA genes in individual ribosomal RNA transcription units of Escherichia coli., Proc Natl Acad Sci U S A 74(7):2710-4
[62] 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
[63] 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
[64] Muth GW., Chen L., Kosek AB., Strobel SA., 2001, pH-dependent conformational flexibility within the ribosomal peptidyl transferase center., RNA 7(10):1403-15
[65] Muto A., 1975, Preferential ribosomal RNA synthesis in the lysate of Escherichia coli., Mol Gen Genet 138(1):1-10
[66] Muto A., 1977, Control of ribosomal RNA synthesis in Escherichia coli. II. Ribosomal RNA synthesis in isolated nucleoids., Mol Gen Genet 152(3):153-9
[67] Muto A., 1977, Control of ribosomal RNA synthesis in Escherichia coli. III. Cytoplasmic factors for ribosomal RNA synthesis., Mol Gen Genet 152(3):161-5
[68] 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
[69] Nisen P., Shapiro L., null, E. coli ribosomal RNA contains sequences homologous to insertion sequences IS1 and IS2., Nature 282(5741):872-4
[70] 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
[71] 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
[72] 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
[73] Pfeiffer T., Hartmann RK., 1997, Role of the spacer boxA of Escherichia coli ribosomal RNA operons in efficient 23 S rRNA synthesis in vivo., J Mol Biol 265(4):385-93
[74] Polacek N., Barta A., 1998, Metal ion probing of rRNAs: evidence for evolutionarily conserved divalent cation binding pockets., RNA 4(10):1282-94
[75] Polach KJ., Uhlenbeck OC., 2002, Cooperative binding of ATP and RNA substrates to the DEAD/H protein DbpA., Biochemistry 41(11):3693-702
[76] 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
[77] Reiness G., Yang HL., Zubay G., Cashel M., 1975, Effects of guanosine tetraphosphate on cell-free synthesis of Escherichia coli ribosomal RNA and other gene products., Proc Natl Acad Sci U S A 72(8):2881-5
[78] 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
[79] 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
[80] Schindler DG., Davies JE., 1977, Specific cleavage of ribosomal RNA caused by alpha sarcin., Nucleic Acids Res 4(4):1097-1110
[81] 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
[82] Sekiya T., Mori M., Takahashi N., Nishimura S., 1980, Sequence of the distal tRNA1Asp gene and the transcription termination signal in the Escherichia coli ribosomal RNA operon rrnF(or G)., Nucleic Acids Res 8(17):3809-27
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[86] Siehnel RJ., Morgan EA., 1985, Unbalanced rRNA gene dosage and its effects on rRNA and ribosomal-protein synthesis., J Bacteriol 163(2):476-86
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[88] Steen R., Dahlberg AE., Lade BN., Studier FW., Dunn JJ., 1986, T7 RNA polymerase directed expression of the Escherichia coli rrnB operon., EMBO J 5(5):1099-103
[89] 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
[90] 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
[91] Szymkowiak C., Wagner R., 1987, Effects of deletions in the spacer region of the rrnB operon on the transcription of the large ribosomal RNAs from Escherichia coli., Mol Microbiol 1(3):327-34
[92] 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
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[94] Tewari DS., Burma DP., 1983, Incorporation of 5S RNA into 16S-23S RNA complex., Biochem Biophys Res Commun 114(1):348-54
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[96] Theissen G., Eberle J., Zacharias M., Tobias L., Wagner R., 1990, The tL structure within the leader region of Escherichia coli ribosomal RNA operons has post-transcriptional functions., Nucleic Acids Res 18(13):3893-901
[97] Thomas GJ., Prescott B., Hamilton MG., 1980, Raman spectra and conformational properties of ribosomes during various stages of disassembly., Biochemistry 19(15):3604-13
[98] 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
[99] 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
[100] 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
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[108] 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
[109] 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
[110] 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
[111] Zacharias M., Wagner R., 1989, Functional characterization of a putative internal promoter sequence between the 16S and the 23S RNA genes within the Escherichia coli rrnB operon., Mol Microbiol 3(3):405-10
[112] Zacharias M., Wagner R., 1987, Deletions in the tL structure upstream to the rRNA genes in the E. coli rrnB operon cause transcription polarity., Nucleic Acids Res 15(20):8235-48
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