RegulonDB RegulonDB 11.1: Operon Form
   

nanATEKQ operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: nanATEK-yhcH
Gene(s): nanQ, nanK, nanE, nanT, nanA   Genome Browser M3D Gene expression COLOMBOS
Note(s): nanATEK-yhcH, among other genes involved in carbon source transport and metabolism, were downregulated in two MG1655 lysogens carrying closely related Stx2a phages O104 and PA8 1208335|.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
[EXP-IEP-COREGULATION] Inferred through co-regulation
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] Kalivoda KA., et al., 2013
[2] Kalivoda KA., et al., 2003
[3] Ohta Y., et al., 1985
[4] Plumbridge J., et al., 1999
Promoter
Name: nanAp
+1: 3373620
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 44
Sequence: agatcgcattataagctttctgtatggggtgttgcttaattgatctggtataacaggtatAaaggtatatcgtttatcaga
                             -35                      -10   +1                   
Evidence: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Huerta AM., et al., 2003
[6] Imashimizu M., et al., 2020
[2] Kalivoda KA., et al., 2003
[3] Ohta Y., et al., 1985
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 nanAp 3373670 3373691 -60.5 ataatgccacTTTAGTGAAGCAGATCGCATTAtaagctttct nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]
[Fis,-] 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 Fis repressor nanAp 3373593 3373612 19.0 ataaaggtatATCGTTTATCAGACAAGCATcacttcagag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
proximal Fis repressor nanAp 3373634 3373653 -23.0 ttctgtatggGGTGTTGCTTAATTGATCTGgtataacagg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
proximal Fis repressor nanAp 3373663 3373682 -52.0 ctttagtgaaGCAGATCGCATTATAAGCTTtctgtatggg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
[NanR,-] 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 NanR repressor nanAp 3373612 3373617 6.5 caggtataaaGGTATAtcgtttatca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [4]
proximal NanR repressor nanAp 3373620 3373625 -2.5 tggtataacaGGTATAaaggtatatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [4]
proximal NanR repressor nanAp 3373629 3373634 -11.5 taattgatctGGTATAacaggtataa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [4]


Transcription unit          
Name: nanA
Gene(s): nanA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Kalivoda KA., et al., 2013
Promoter
Name: nanAp
+1: 3373620
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 44
Sequence: agatcgcattataagctttctgtatggggtgttgcttaattgatctggtataacaggtatAaaggtatatcgtttatcaga
                             -35                      -10   +1                   
Evidence: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [5] Huerta AM., et al., 2003
[6] Imashimizu M., et al., 2020
[2] Kalivoda KA., et al., 2003
[3] Ohta Y., et al., 1985
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 nanAp 3373670 3373691 -60.5 ataatgccacTTTAGTGAAGCAGATCGCATTAtaagctttct nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [2]
[Fis,-] 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 Fis repressor nanAp 3373593 3373612 19.0 ataaaggtatATCGTTTATCAGACAAGCATcacttcagag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
proximal Fis repressor nanAp 3373634 3373653 -23.0 ttctgtatggGGTGTTGCTTAATTGATCTGgtataacagg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
proximal Fis repressor nanAp 3373663 3373682 -52.0 ctttagtgaaGCAGATCGCATTATAAGCTTtctgtatggg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
[NanR,-] 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 NanR repressor nanAp 3373612 3373617 6.5 caggtataaaGGTATAtcgtttatca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [4]
proximal NanR repressor nanAp 3373620 3373625 -2.5 tggtataacaGGTATAaaggtatatc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [4]
proximal NanR repressor nanAp 3373629 3373634 -11.5 taattgatctGGTATAacaggtataa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [4]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -16.7 3372584 3372613 aattttcataCCAAAGCGTGTGGGCATCGCCCACCGCGGgagactcaca
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    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA] Inferred from direct assay

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

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Kalivoda KA., Steenbergen SM., Vimr ER., 2013, Control of the Escherichia coli sialoregulon by transcriptional repressor NanR., J Bacteriol 195(20):4689-701

 [2] Kalivoda KA., Steenbergen SM., Vimr ER., Plumbridge J., 2003, Regulation of sialic acid catabolism by the DNA binding protein NanR in Escherichia coli., J Bacteriol 185(16):4806-15

 [3] Ohta Y., Watanabe K., Kimura A., 1985, Complete nucleotide sequence of the E. coli N-acetylneuraminate lyase., Nucleic Acids Res 13(24):8843-52

 [4] Plumbridge J., Vimr E., 1999, Convergent pathways for utilization of the amino sugars N-acetylglucosamine, N-acetylmannosamine, and N-acetylneuraminic acid by Escherichia coli., J Bacteriol 181(1):47-54

 [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] Imashimizu M., Tokunaga Y., Afek A., Takahashi H., Shimamoto N., Lukatsky DB., 2020, Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences., Biomolecules 10(9)

 [7] Bradley MD., Beach MB., de Koning AP., Pratt TS., Osuna R., 2007, Effects of Fis on Escherichia coli gene expression during different growth stages., Microbiology 153(Pt 9):2922-40

 [8] Beisel CL., Storz G., 2011, The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli., Mol Cell 41(3):286-97

 [9] Beisel CL., Updegrove TB., Janson BJ., Storz G., 2012, Multiple factors dictate target selection by Hfq-binding small RNAs., EMBO J 31(8):1961-74

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