RegulonDB RegulonDB 10.9: Operon Form
   

rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-secY-rpmJ operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-secY-rpmJ
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-secY-rpmJ
Synonym(s): rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-prlA-rpmJ, spc
Gene(s): rpmJ, secY, rplO, rpmD, rpsE, rplR, rplF, rpsH, rpsN, rplE, rplX, rplN   Genome Browser M3D Gene expression COLOMBOS
Evidence: [PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Cerretti DP., et al., 1983
Promoter
Name: rplNp
+1: 3448222
Distance from start of the gene: 73
Sequence: ctcagaaatgagccgtttattttttctacccatatccttgaagcggtgttataatgccgcGccctcgatatggggattttt
Evidence: [CV(RPF/RS-EPT-CBR)]
[RPF]
[RS-EPT-CBR]
Reference(s): [2] Post LE., et al., 1978
[3] Post LE., et al., 1978
[4] Salgado H, et al., 2012
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition rplNp nd 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


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -20.0 3448256 3448291 tctcaatacgAATAAACGGCTCAGAAATGAGCCGTTTATTTTTTCtacccatatc
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"


Evidence    

 [CV(RPF/RS-EPT-CBR)] cross validation(RPF/RS-EPT-CBR)

 [RPF] RNA polymerase footprinting

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Cerretti DP., Dean D., Davis GR., Bedwell DM., Nomura M., 1983, The spc ribosomal protein operon of Escherichia coli: sequence and cotranscription of the ribosomal protein genes and a protein export gene., Nucleic Acids Res 11(9):2599-616

 [2] Post LE., Arfsten AE., Nomura M., Jaskunas SR., 1978, Isolation and characterization of a promoter mutant in the str ribosomal protein operon in E. coli., Cell 15(1):231-6

 [3] Post LE., Arfsten AE., Reusser F., Nomura M., 1978, DNA sequences of promoter regions for the str and spc ribosomal protein operons in E. coli., Cell 15(1):215-29

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [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

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