RegulonDB RegulonDB 10.9: Operon Form
   

rpsMKD-rpoA-rplQ operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: rpsMKD-rpoA-rplQ
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: rpsMKD-rpoA-rplQ
Gene(s): rplQ, rpoA, rpsD, rpsK, rpsM   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ITCR] Inferred through co-regulation
Reference(s): [1] Jaskunas SR., et al., 1975
Promoter
Name: rpsMp1
+1: 3442495
Distance from start of the gene: 24
Sequence: tgtatgtctgtgcgtttccatttgagtatcctgaaaacgggcttttcagcatggaacgtaCatattaaatagtaggagtgc
Evidence: [HTTIM]
Reference(s): [2] Mendoza-Vargas A., et al., 2009
Terminator(s)
Type: rho-independent
Sequence: gtataaaaaaACCCGCCGGGGCGGGtttttttacg
Reference(s): [3] Bedwell D., et al., 1985


Transcription unit       
Name: rpsMKD-rpoA-rplQ
Gene(s): rplQ, rpoA, rpsD, rpsK, rpsM   Genome Browser M3D Gene expression COLOMBOS
Evidence: [ITCR] Inferred through co-regulation
[PM] Polar mutation
Reference(s): [1] Jaskunas SR., et al., 1975
[4] Meek DW., et al., 1984
[5] Post LE., et al., 1980
Promoter
Name: rpsMp2
+1: 3442565
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 94
Sequence: aaggctgattttttcgcatatttttcttgcaaagttgggttgagctggctagattagccaGccaatcttttgtatgtctgt
                           -35                    -10       +1                   
Note(s): This promoter appears to be induced in two phases after σE induction. It is induced during the first 5 minutes following σE induction, decreased from 5 to 10 minutes, induced from 10 to 15 minutes, and decreased from 15 to 20 minutes Lacoux C,2020.
Evidence: [HIPP]
[HTTIM]
[ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [6] Huerta AM., et al., 2003
[2] Mendoza-Vargas A., et al., 2009
[5] Post LE., et al., 1980
[7] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: gtataaaaaaACCCGCCGGGGCGGGtttttttacg
Reference(s): [3] Bedwell D., et al., 1985
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA-ppGpp inhibition rpsMp2 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]
[8]
Evidence: [APPH] Assay of protein purified to homogeneity
[GEA] Gene expression analysis
[IMP] Inferred from mutant phenotype
Reference(s): [8] 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 -16.9 3442553 3442588 tgcaaagttgGGTTGAGCTGGCTAGATTAGCCAGCCAATCTTTTGtatgtctgtg
  anti-terminator -4.3 3442573 3442601 cgcatattttTCTTGCAAAGTTGGGTTGAGCTGGCTAGattagccagc
  anti-anti-terminator -6.53 3442588 3442644 cagtgccgagCCGAAGCATAAACAGCGCCAAGGCTGATTTTTTCGCATATTTTTCTTGCAAAGTTGggttgagctg
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"
REGULATION, RNA cis-regulatory element:  
Rfam type: Cis-reg
Strand: reverse
Evidence: [ICA] Inferred by computational analysis
Reference(s): [9] null null
  Description Rfam score Left Pos Right Pos Sequence (RNA-strand)
  Alpha operon ribosome binding site 104.1 3442439 3442550 ucuuuuguauGUCUGUGCGUUUCCAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGUAGGAGUGCAUAGUGGCCCGUAUAGCAGGCAUUAACAUUCCUGAUcauaagcaug
Notes: "The provied "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appears as the reverse complement of the sequence delimited by LeftPos-RightPos"




Reference(s)    

 [1] Jaskunas SR., Burgess RR., Nomura M., 1975, Identification of a gene for the alpha-subunit of RNA polymerase at the str-spc region of the Escherichia coli chromosome., Proc Natl Acad Sci U S A 72(12):5036-40

 [2] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [3] Bedwell D., Davis G., Gosink M., Post L., Nomura M., Kestler H., Zengel JM., Lindahl L., 1985, Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli., Nucleic Acids Res 13(11):3891-903

 [4] Meek DW., Hayward RS., 1984, Nucleotide sequence of the rpoA-rplQ DNA of Escherichia coli: a second regulatory binding site for protein S4?, Nucleic Acids Res 12(14):5813-21

 [5] Post LE., Arfsten AE., Davis GR., Nomura M., 1980, DNA sequence of the promoter region for the alpha ribosomal protein operon in Escherichia coli., J Biol Chem 255(10):4653-59

 [6] 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

 [7] 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.

 [8] 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

 [9] null, null, null, null


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