RegulonDB RegulonDB 10.9: Operon Form
   

rplU-rpmA-yhbE-obgE operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: rplU-rpmA-yhbE-obgE
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: rplU-rpmA-yhbE-obgE
Gene(s): obgE, yhbE, rpmA, rplU   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ITCR] Inferred through co-regulation
[LTED] Length of transcript experimentally determined
Reference(s): [1] Maouche R., et al., 2016
Promoter
Name: rplUp
+1: 3333516
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 65
Sequence: ttcttcgtgtattgactgtagcacttgtcaaaggcgtgcgttttgcgtaatattcgcgccCtattgtgaatatttatagcg
                         -35                    -10         +1                   
Evidence: [HIPP]
[ICWHO]
[IHBCE]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[1] Maouche R., et al., 2016
[3] Salgado H, et al., 2012
TF binding sites (TFBSs)
[MlrA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MlrA1 activator rplUp 3333585 3333619 -85.5 attgtactgaAAAAATGGCACAGATAAACGTTACCGTACAAGTTGtgtttttttt nd [APIORCISFBSCS], [BPP] [4]
Note(s): 1The MlrA-rplUp regulatory interaction was identified by sequence analysis reported by Ogasawara et al., and by a gel shift assay using purified transcription factor (data not provided) Ogasawara H,20101The MlrA-rplUp regulatory interaction was identified by sequence analysis reported by Ogasawara et al., and by a gel shift assay using purified transcription factor (data not provided) Ogasawara H,2010
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition rplUp nd The rplU-rpmA operon is regulated by ppGpp-DksA-dependent negative stringent control under amino acid starvation, most likely due to the features of the discriminator region (G/C rich) separating the -10 promoter element from the transcription start site (TSS) Aseev LV,2016. [GEA] [5]
Evidence: [GEA] Gene expression analysis
Reference(s): [5] Aseev LV., et al., 2016


Transcription unit          
Name: rplU-rpmA
Gene(s): rpmA, rplU   Genome Browser M3D Gene expression COLOMBOS
Reference(s): [6] Kitakawa M., et al., 1979
Promoter
Name: rplUp
+1: 3333516
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 65
Sequence: ttcttcgtgtattgactgtagcacttgtcaaaggcgtgcgttttgcgtaatattcgcgccCtattgtgaatatttatagcg
                         -35                    -10         +1                   
Evidence: [HIPP]
[ICWHO]
[IHBCE]
[RS-EPT-CBR]
[TIM]
Reference(s): [2] Huerta AM., et al., 2003
[1] Maouche R., et al., 2016
[3] Salgado H, et al., 2012
TF binding sites (TFBSs)
[MlrA,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MlrA1 activator rplUp 3333585 3333619 -85.5 attgtactgaAAAAATGGCACAGATAAACGTTACCGTACAAGTTGtgtttttttt nd [APIORCISFBSCS], [BPP] [4]
Note(s): 1The MlrA-rplUp regulatory interaction was identified by sequence analysis reported by Ogasawara et al., and by a gel shift assay using purified transcription factor (data not provided) Ogasawara H,20101The MlrA-rplUp regulatory interaction was identified by sequence analysis reported by Ogasawara et al., and by a gel shift assay using purified transcription factor (data not provided) Ogasawara H,2010
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition rplUp nd The rplU-rpmA operon is regulated by ppGpp-DksA-dependent negative stringent control under amino acid starvation, most likely due to the features of the discriminator region (G/C rich) separating the -10 promoter element from the transcription start site (TSS) Aseev LV,2016. [GEA] [5]
Evidence: [GEA] Gene expression analysis
Reference(s): [5] Aseev LV., et al., 2016


Transcription unit       
Name: yhbE-obgE
Gene(s): obgE, yhbE   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ICWHO] Inferred computationally without human oversight


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -18.0 3332806 3332833 acggatgaaaGCCCCGCAACACGTTGCGGGGCTTTTTacattcgata
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    

 [HIPP] Human inference of promoter position

 [ICWHO] Inferred computationally without human oversight

 [IHBCE] Inferred by a human based on computational evidence

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

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins


Reference(s)    

 [1] Maouche R., Burgos HL., My L., Viala JP., Gourse RL., Bouveret E., 2016, Coexpression of Escherichia coli obgE, Encoding the Evolutionarily Conserved Obg GTPase, with Ribosomal Proteins L21 and L27., J Bacteriol 198(13):1857-67

 [2] 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

 [3] 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.

 [4] Ogasawara H., Yamamoto K., Ishihama A., 2010, Regulatory role of MlrA in transcription activation of csgD, the master regulator of biofilm formation in Escherichia coli., FEMS Microbiol Lett 312(2):160-8

 [5] Aseev LV., Koledinskaya LS., Boni IV., 2016, Regulation of Ribosomal Protein Operons rplM-rpsI, rpmB-rpmG, and rplU-rpmA at the Transcriptional and Translational Levels., J Bacteriol 198(18):2494-502

 [6] Kitakawa M., Dabbs ER., Isono K., 1979, Genes coding for ribosomal proteins S15, L21, and L27 map near argG in Escherichia coli., J Bacteriol 138(3):832-8

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