RegulonDB RegulonDB 11.1: Gene Form
   

rrfD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rrlD rrfD thrV rrfFp2 rrfFp2

Gene      
Name: rrfD    Texpresso search in the literature
Synonym(s): ECK3261, EG30073, b3274
Genome position(nucleotides): 3423668 <-- 3423787
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 64.17
External database links:  
ASAP:
 ABE-0010744
ECHOBASE:
 EB4236
ECOLIHUB:
 rrfD
OU-MICROARRAY:
 b3274
COLOMBOS: rrfD


Product      
Name: 5S ribosomal RNA
Synonym(s): 5S rRNA, rrfD, rrfD 5S ribosomal RNA
Type: rRNA
Cellular location: cytosol
Classification:
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] Abdukaiumov M., et al., 1987
[2] Albrechtsen B., et al., 1991
[3] Ammons D., et al., 1999
[4] Aubert M., et al., 1973
[5] Bailey SC., et al., 1979
[6] Brosius J., et al., 1984
[7] Doctor BP., et al., 1972
[8] Doolittle WF., et al., 1970
[9] Duester GL., et al., 1980
[10] Feunteun J., et al., 1970
[11] Fraser RS., et al., 1975
[12] Galibert F., et al., 1971
[13] Garrett RA., et al., 1974
[14] Glotz C., et al., 1981
[15] Gorelic L., et al., 1978
[16] Hernandez F., et al., 1975
[17] Jarry B., et al., 1973
[18] Jarry B., et al., 1973
[19] Jarry B., et al., 1970
[20] Jarry B., et al., 1971
[21] Jordan B., et al., 1969
[22] Kaiser II. 1970
[23] Kakegawa T., et al., 1986
[24] Karpel RL., et al., 1982
[25] Kim J., et al., 1991
[26] Liebke H., et al., 1985
[27] Merryman C., et al., 1999
[28] Morgan EA., et al., 1978
[29] Murphy JC., et al., 2001
[30] Muto A. 1977
[31] Orosz A., et al., 1991
[32] Pace B., et al., 1971
[33] Philipps GR., et al., 1972
[34] Robins HI., et al., 1968
[35] Sarmientos P., et al., 1983
[36] Schulze H., et al., 1982
[37] Scott JF., et al., 1968
[38] Seol W., et al., 1990
[39] Shen V., et al., 1977
[40] Srivastava AK., et al., 1991
[41] Steen R., et al., 1986
[42] Teixido J., et al., 1989
[43] Usary J., et al., 2001
[44] Vola C., et al., 1977
[45] Yamamoto M., et al., 1976
[46] Yu RS. 1973
[47] Yuan D., et al., 1975
External database links:  
ECOCYC:
 RRFD-RRNA
ECOLIWIKI:
 b3274


Operon      
Name: rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF         
Operon arrangement:
Transcription unit        Promoter
rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF
rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF
rrsD-ileU-alaU-rrlD-rrfD-thrV-rrfF


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 rrfFp2 3423707 reverse nd [COMP-AINF] [48]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Abdukaiumov M., Gimautdinova OI., Graifer DM., Zenkova MA., Karpova GG., 1987, [Preparation of Escherichia coli 70S ribosomes labeled with 35S], Biokhimiia 52(9):1411-6

 [2] Albrechtsen B., Ross BM., Squires C., Squires CL., 1991, Transcriptional termination sequence at the end of the Escherichia coli ribosomal RNA G operon: complex terminators and antitermination., Nucleic Acids Res 19(8):1845-52

 [3] Ammons D., Rampersad J., Fox GE., 1999, 5S rRNA gene deletions cause an unexpectedly high fitness loss in Escherichia coli., Nucleic Acids Res 27(2):637-42

 [4] Aubert M., Bellemare G., Monier R., 1973, Selective reaction of glyoxal with guanine residues in native and denatured Escherichia coli 5S RNA., Biochimie 55(2):135-42

 [5] Bailey SC., Apirion D., 1979, Repetitive DNA in Escherichia coli: multiple sequences complementary to small stable RNAs., Mol Gen Genet 172(3):339-43

 [6] Brosius J., Holy A., 1984, Regulation of ribosomal RNA promoters with a synthetic lac operator., Proc Natl Acad Sci U S A 81(22):6929-33

 [7] 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

 [8] Doolittle WF., Pace NR., 1970, Synthesis of 5S ribosomal RNA in Escherichia coli after rifampicin treatment., Nature 228(267):125-9

 [9] Duester GL., Holmes WM., 1980, The distal end of the ribosomal RNA operon rrnD of Escherichia coli contains a tRNA1thr gene, two 5s rRNA genes and a transcription terminator., Nucleic Acids Res 8(17):3793-807

 [10] 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

 [11] 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

 [12] 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

 [13] 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

 [14] 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

 [15] 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

 [16] Hernandez F., Vazquez D., Ballesta JP., 1975, Partial reconstitution of active ribosomes and 50S subunits., Biochemistry 14(7):1503

 [17] Jarry B., Rosset R., 1973, Localization of some 5s RNA cistrons on Escherichia coli chromosome., Mol Gen Genet 121(2):151-62

 [18] Jarry B., Rosset R., 1973, Further mapping of 5S RNA cistrons in Escherichia coli., Mol Gen Genet 126(1):29-35

 [19] Jarry B., Rosset R., 1970, An attempt to localize 5S RNA cistrons in Escherichia coli., Biochem Biophys Res Commun 41(3):789-96

 [20] Jarry B., Rosset R., 1971, Heterogeneity of 5S RNA in Escherichia coli., Mol Gen Genet 113(1):43-50

 [21] Jordan B., Forget B., 1969, [Identification of the properties of a 5S RNA synthesized by E. coli in the presence of chloramphenicol], Bull Soc Chim Biol (Paris) 51(10):1541

 [22] Kaiser II., 1970, Isolation of 5-fluorouracil-containing 5S ribonucleic acid from Escherichia coli., Biochemistry 9(3):569-73

 [23] 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

 [24] Karpel RL., Miller NS., Fresco JR., 1982, Mechanistic studies of ribonucleic acid renaturation by a helix-destabilizing protein., Biochemistry 21(9):2102-8

 [25] Kim J., Cheong C., Moore PB., 1991, Tetramerization of an RNA oligonucleotide containing a GGGG sequence., Nature 351(6324):331-2

 [26] Liebke H., Hatfull G., 1985, The sequence of the distal end of the E. coli ribosomal RNA rrnE operon indicates conserved features are shared by rrn operons., Nucleic Acids Res 13(15):5515-25

 [27] Merryman C., Moazed D., Daubresse G., Noller HF., 1999, Nucleotides in 23S rRNA protected by the association of 30S and 50S ribosomal subunits., J Mol Biol 285(1):107-13

 [28] 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

 [29] Murphy JC., Fox GE., Willson RC., 2001, RNA isolation and fractionation with compaction agents., Anal Biochem 295(2):143-8

 [30] 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

 [31] Orosz A., Boros I., Venetianer P., 1991, Analysis of the complex transcription termination region of the Escherichia coli rrnB gene., Eur J Biochem 201(3):653-9

 [32] Pace B., Pace NR., 1971, Gene dosage for 5S ribosomal ribonucleic acid in Escherichia coli ad Bacillus megaterium., J Bacteriol 105(1):142-9

 [33] Philipps GR., Timko JL., 1972, Simple method for the characterization of 5S RNA., Anal Biochem 45(1):319-25

 [34] Robins HI., Raacke ID., 1968, A simplified procedure for the simultaneous isolation of 4S and 5S RNA., Biochem Biophys Res Commun 33(2):240-6

 [35] Sarmientos P., Sylvester JE., Contente S., Cashel M., 1983, Differential stringent control of the tandem E. coli ribosomal RNA promoters from the rrnA operon expressed in vivo in multicopy plasmids., Cell 32(4):1337-46

 [36] Schulze H., Nierhaus KH., 1982, Minimal set of ribosomal components for reconstitution of the peptidyltransferase activity., EMBO J 1(5):609-13

 [37] Scott JF., Monier R., Aubert M., Reynier M., 1968, Some optical properties of 5S-RNA from E. coli., Biochem Biophys Res Commun 33(5):794-800

 [38] Seol W., Shatkin AJ., 1990, Sequence of the distal end of E. coli ribosomal RNA rrnG operon., Nucleic Acids Res 18(10):3056

 [39] Shen V., Bremer H., 1977, Rate of ribosomal ribonucleic acid chain elongation in Escherichia coli B/r during chloramphenicol treatment., J Bacteriol 130(3):1109-16

 [40] Srivastava AK., Schlessinger D., 1991, Structure and organization of ribosomal DNA., Biochimie 73(6):631-8

 [41] 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

 [42] Teixido J., Altamura S., Londei P., Amils R., 1989, Structural and functional exchangeability of 5 S RNA species from the eubacterium E.coli and the thermoacidophilic archaebacterium Sulfolobus solfataricus., Nucleic Acids Res 17(3):845-51

 [43] Usary J., Champney WS., 2001, Erythromycin inhibition of 50S ribosomal subunit formation in Escherichia coli cells., Mol Microbiol 40(4):951-62

 [44] Vola C., Jarry B., Rosset R., 1977, Linkage of 5S RNA and 16S+23S RNA genes on the E. coli chromosome., Mol Gen Genet 153(3):337-41

 [45] Yamamoto M., Lindahl L., Nomura M., 1976, Synthesis of ribosomal RNA in E. coli: analysis using deletion mutants of a lambda transducing phage carrying ribosomal RNA genes., Cell 7(2):179-90

 [46] Yu RS., 1973, A simple method for the preparation of 5S RNA from Escherichia coli., Hoppe Seylers Z Physiol Chem 354(2):125-30

 [47] 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

 [48] 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

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