RegulonDB RegulonDB 10.8: Operon Form
   

rplKAJL-rpoBC operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: rplKAJL-rpoBC
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: rplKAJL-rpoBC
Gene(s): rplK, rplA, rplJ, rplL, rpoB, rpoC   Genome Browser M3D Gene expression COLOMBOS
Note(s): There has been identified an attenuator that stops 70% of the transcription starts. It is located between the rplL and rpoB genes Post LE,1979. Ralling G,1984.
Evidence: [PM] Polar mutation
Reference(s): [1] Steward KL., et al., 1991
Promoter
Name: rplKp
+1: 4178354
Distance from start of the gene: 93
Sequence: cgatcaaaaaagcggcgatttaatcgttgcacaaggcgtgagattggaatacaatttcgcGccttttgtttttatgggcct
Note(s): Promoters rplJp and rplKp were identified in in vitro experiments that assigned possible start sites Post LE,1979. They appear to be the major promoters within the rplKLJL-rpoBC operon, although rplKp is 35% stronger than rplJp Ralling G,1984.
Evidence: [HIPP]
[IMP]
[TIM]
Reference(s): [2] Post LE., et al., 1979
[3] Yamamoto M., et al., 1979
Terminator(s)
Type: rho-independent
Sequence: taacgtaaaaACCCGCTTCGGCGGGtttttttatg
Reference(s): [4] Squires C., et al., 1981
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition rplKp Together ppGpp and DksA can inhibit more strongly the transcription initiation from the ribosomal protein promoter in vitro and in vivo Lemke JJ,2011 [APPH]
[GEA]
[IMP]
[5]
Evidence: [APPH] Assay of protein purified to homogeneity
[GEA] Gene expression analysis
[IMP] Inferred from mutant phenotype
Reference(s): [5] Lemke JJ., et al., 2011


Transcription unit       
Name: rplJL-rpoBC
Gene(s): rplJ, rplL, rpoB, rpoC   Genome Browser M3D Gene expression COLOMBOS
Note(s): rplJL-rpoBC here has been identified as an attenuator that stops 70% of the transcription starts, and it is located between the rplL and rpoB genes Post LE,1979. Ralling G,1984.
Evidence: [PM] Polar mutation
Reference(s): [6] Barry G., et al., 1980
[7] Hui I., et al., 1982
Promoter
Name: rplJp
+1: 4179623
Distance from start of the gene: 373
Sequence: ctgagcgcttctgtaaactaatgcctttacgtgggcggtgattttgtctacaatcttaccCccacgtataatgcttaatgc
Note(s): Promoters rplJp and rplKp were identified using in vitro experiments that assign possible start sites Post LE,1979. They appear to be the major promoters within the rplKLJL-rpoBC operon, although rplKp is 35 % stronger than rplJp Ralling G,1984.
Evidence: [HIPP]
[IMP]
[TIM]
Reference(s): [2] Post LE., et al., 1979
Terminator(s)
Type: rho-independent
Sequence: taacgtaaaaACCCGCTTCGGCGGGtttttttatg
Reference(s): [4] Squires C., et al., 1981
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition rplJp Together ppGpp and DksA can inhibit more strongly the transcription initiation from the ribosomal protein promoter in vitro and in vivo Lemke JJ,2011 [APPH]
[GEA]
[IMP]
[5]
Evidence: [APPH] Assay of protein purified to homogeneity
[GEA] Gene expression analysis
[IMP] Inferred from mutant phenotype
Reference(s): [5] Lemke JJ., et al., 2011


Transcription unit       
Name: rpoBC
Gene(s): rpoB, rpoC   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [6] Barry G., et al., 1980
[8] Fukuda R., et al., 1983
Promoter
Name: rpoBp
+1: 4181063
Distance from start of the gene: 182
Sequence: aaggcgccagtagcgtttcacactgtttgactactgctgtgcctttcaatgcttgtttctAtcgacgacttaatatactgc
Note(s): The rpoBp promoter is very weak; as a matter of fact, Ralling and Linn Ralling G,1984did not find evidence for it. Therefore, it can be concluded that even if it does exist, it might not be very efficient.
Evidence: [NAS]
[TIM]
Reference(s): [9] Bass IA., et al., null
[8] Fukuda R., et al., 1983
Terminator(s)
Type: rho-independent
Sequence: taacgtaaaaACCCGCTTCGGCGGGtttttttatg
Reference(s): [4] Squires C., et al., 1981


Transcription unit       
Name: rplL
Gene(s): rplL   Genome Browser M3D Gene expression COLOMBOS
Note(s): Due to the attenuator identified between the rplL and rpoB genes, and its weak promoter, rplLp, the transcription rate of this transciption unit (rpoBC) is very low Ralling G,1984.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [10] Ralling G., et al., 1984
Promoter
Name: rplLp
+1: Unknown
Note(s): rplLp is a weak promoter; it is only 8% as effective as the rplJp promoter Ralling G,1984
Evidence: [IEP]
[IMP]
Reference(s): [10] Ralling G., et al., 1984
[11] Zaslaver A., et al., 2006


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -21.6 4178323 4178368 taatcgttgcACAAGGCGTGAGATTGGAATACAATTTCGCGCCTTTTGTTTTTATgggccttgcc
  terminator -6.2 4180484 4180510 tgcgaaagaaGCTGCTTAATCGCAGTTATCTTTTTAacgcattcgc
  terminator -12.4 4185317 4185351 aacccggcagCGGATTGTGCTAACTCCGACGGGAGCAAATCCGTgaaagattta
  anti-terminator -8.13 4178294 4178339 ctaacccagcGATCAAAAAAGCGGCGATTTAATCGTTGCACAAGGCGTGAGATTGgaatacaatt
  anti-terminator -7.3 4180460 4180490 tcgtactctgGCTGCTGTACGCGATGCGAAAGAAGCTGCTtaatcgcagt
  anti-anti-terminator -18.6 4178238 4178313 tctatcttcgGTCGTGCGACCCCGGTAGAGCTGGACTTCAGCCAGGTTGAAAAAGCCTAACCCAGCGATCAAAAAAGCGGCGATTtaatcgttgc
  anti-anti-terminator -3.6 4180452 4180471 aaactggttcGTACTCTGGCTGCTGTACGcgatgcgaaa
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"




Reference(s)    

 [1] Steward KL., Linn T., 1991, In vivo analysis of overlapping transcription units in the rplKAJLrpoBC ribosomal protein-RNA polymerase gene cluster of Escherichia coli., J Mol Biol 218(1):23-31

 [2] Post LE., Strycharz GD., Nomura M., Lewis H., Dennis PP., 1979, Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli., Proc Natl Acad Sci U S A 76(4):1697-701

 [3] Yamamoto M., Nomura M., 1979, Organization of genes for transcription and translation in the rif region of the Escherichia coli chromosome., J Bacteriol 137(1):584-94

 [4] Squires C., Krainer A., Barry G., Shen WF., Squires CL., 1981, Nucleotide sequence at the end of the gene for the RNA polymerase beta' subunit (rpoC)., Nucleic Acids Res 9(24):6827-40

 [5] Lemke JJ., Sanchez-Vazquez P., Burgos HL., Hedberg G., Ross W., Gourse RL., 2011, Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA., Proc Natl Acad Sci U S A 108(14):5712-7

 [6] Barry G., Squires C., Squires CL., 1980, Attenuation and processing of RNA from the rplJL--rpoBC transcription unit of Escherichia coli., Proc Natl Acad Sci U S A 77(6):3331-5

 [7] Hui I., Maltman K., Little R., Hastrup S., Johnsen M., Fiil N., Dennis P., 1982, Insertions of transposon Tn5 into ribosomal protein PNA polymerase operons., J Bacteriol 152(3):1022-32

 [8] Fukuda R., Nagasawa-Fujimori H., 1983, Mechanism of the rifampicin induction of RNA polymerase beta and beta' subunit synthesis in Escherichia coli., J Biol Chem 258(4):2720-8

 [9] Bass IA., Kurenova EV., Mekhedov SL., null, [Cloning of the promoter of the RNA polymerase operon located before the structural gene of the beta-subunit], Mol Biol (Mosk) 16(3):575-80

 [10] Ralling G., Linn T., 1984, Relative activities of the transcriptional regulatory sites in the rplKAJLrpoBC gene cluster of Escherichia coli., J Bacteriol 158(1):279-85

 [11] Zaslaver A., Bren A., Ronen M., Itzkovitz S., Kikoin I., Shavit S., Liebermeister W., Surette MG., Alon U., 2006, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli., Nat Methods 3(8):623-8


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