RegulonDB RegulonDB 11.1: Operon Form
   

sfsA-dksA-gluQ operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: sfsA-dksA-gluQ
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: dksA-yadB
Gene(s): gluQ, dksA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on gene expression analysis, it was shown that dksA expression is controlled by YqhC Turner PC,2011
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Dubois DY., et al., 2004
[2] Kang PJ., et al., 1990
Promoter
Name: dksAp2
+1: 160657
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 53
Sequence: ttgtcaagtgttacgtttagataattgctatccggaaaagcatctgctatttatagcggcCtcatttttcccccgaacatg
                              -35                    -10    +1                   
Note(s): Through inhibition of its own transcription, DksA creates a negative feedback loop that keeps its level constant in the cell Chandrangsu P,2011 Regulation of the dksAp2 promoter prevents accumulation of DksA in stationary phase Chandrangsu P,2011
dksA is also regulated by CsrA, but this effect is masked by autoregulation by DksA Edwards AN,2011. DksA negative autoregulation occurs independently of CsrA regulation Edwards AN,2011.
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [3] Chandrangsu P., et al., 2011
[4] Edwards AN., et al., 2011
[5] Huerta AM., et al., 2003
[2] Kang PJ., et al., 1990
[6] Salgado H, et al., 2012
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA inhibition dksAp2 nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[3]
[4]
  DksA-ppGpp inhibition dksAp2 nd   [EXP-IDA-PURIFIED-PROTEIN]
[EXP-IEP-GENE-EXPRESSION-ANALYSIS]
[EXP-IMP] 		[3]
  ppGpp inhibition dksAp2 nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [3]
Evidence: [EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [3] Chandrangsu P., et al., 2011
[4] Edwards AN., et al., 2011


Transcription unit       
Name: dksA-yadB
Gene(s): gluQ, dksA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Dubois DY., et al., 2004
[2] Kang PJ., et al., 1990
Promoter
Name: dksAp1
+1: 160722
Distance from start of the gene: 118
Sequence: gtaaagtaagtaactggttaatttacattctggtcgcgtgcgcaaatacgcttttcctcaCacagttgtcaagtgttacgt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Kang PJ., et al., 1990
[7] Zaslaver A., et al., 2006


Transcription unit       
Name: dksA-gluQ
Gene(s): gluQ, dksA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Dubois DY., et al., 2004
[2] Kang PJ., et al., 1990
Promoter
Name: dksAp3
+1: 160751
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 147
Sequence: cttaaaaaatcactgccggttacattgtagtaaagtaagtaactggttaatttacattctGgtcgcgtgcgcaaatacgct
                              -35                    -10    +1                   
Evidence: [COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [8] Chandrangsu P., et al., 2012


Transcription unit          
Name: sfsA-dksA
Gene(s): dksA, sfsA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [2] Kang PJ., et al., 1990
[9] Kawamukai M., et al., 1991
[10] Yamanaka K., et al., 1994
Promoter
Name: sfsAp
+1: 161515
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 29
Sequence: accctttacgcctcctcgtttgcccgtggacgcacacgctacacgccgctaaaacgctggGcgctaacgcaataacaagga
                                -35                    -10  +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [5] Huerta AM., et al., 2003
[9] Kawamukai M., et al., 1991
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator sfsAp 161570 161592 -65.5 aactggtcgtATGCGGTGACGGAGTTCACCCTTtacgcctcct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [9], [11]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

 [EXP-IEP] Inferred from expression pattern

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


Reference(s)    

 [1] Dubois DY., Blaise M., Becker HD., Campanacci V., Keith G., Giege R., Cambillau C., Lapointe J., Kern D., 2004, An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNAAsp., Proc Natl Acad Sci U S A 101(20):7530-5

 [2] Kang PJ., Craig EA., 1990, Identification and characterization of a new Escherichia coli gene that is a dosage-dependent suppressor of a dnaK deletion mutation., J Bacteriol 172(4):2055-64

 [3] Chandrangsu P., Lemke JJ., Gourse RL., 2011, The dksA promoter is negatively feedback regulated by DksA and ppGpp., Mol Microbiol 80(5):1337-48

 [4] Edwards AN., Patterson-Fortin LM., Vakulskas CA., Mercante JW., Potrykus K., Vinella D., Camacho MI., Fields JA., Thompson SA., Georgellis D., Cashel M., Babitzke P., Romeo T., 2011, Circuitry linking the Csr and stringent response global regulatory systems., Mol Microbiol 80(6):1561-80

 [5] 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

 [6] 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.

 [7] 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

 [8] Chandrangsu P., Wang L., Choi SH., Gourse RL., 2012, Suppression of a dnaKJ deletion by multicopy dksA results from non-feedback-regulated transcripts that originate upstream of the major dksA promoter., J Bacteriol 194(6):1437-46

 [9] Kawamukai M., Utsumi R., Takeda K., Higashi A., Matsuda H., Choi YL., Komano T., 1991, Nucleotide sequence and characterization of the sfs1 gene: sfs1 is involved in CRP*-dependent mal gene expression in Escherichia coli., J Bacteriol 173(8):2644-8

 [10] Yamanaka K., Mitani T., Ogura T., Niki H., Hiraga S., 1994, Cloning, sequencing, and characterization of multicopy suppressors of a mukB mutation in Escherichia coli., Mol Microbiol 13(2):301-12

 [11] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

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