RegulonDB RegulonDB 11.1: Operon Form
   

glnK-amtB operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: glnK-amtB
Gene(s): glnK, amtB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of the glnK-amtB operon is regulated by nitrogen availability; while nitrogen limitation causes operon expression, nitrogen excess represses completely the operon expression Tondervik A,2006
Under nitrogen-rich growth conditions, the expression of the glnK gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased Kumar R,2011
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] van Heeswijk WC., et al., 1996
Promoter
Name: glnKp
+1: 472556
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 42
Sequence: ttaacttcctgctctctttctcgtttttcatttctggcacaccgcttgcaataccttcttCgtgtagcagaaccattaccg
                                   -24         -12          +1                   
Note(s): We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [2] Huerta AM., et al., 2003
[3] Reitzer L., et al., 2001
[1] van Heeswijk WC., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: caagcactgcAAAAAACAGCCGGACGGTTTTCACCTCCGGCTATTTTTTtaattgtgat
Reference(s): [1] van Heeswijk WC., et al., 1996
TF binding sites (TFBSs)
[FNR,+] 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
nd FNR activator glnKp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]
[FNR,-] 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
nd FNR repressor glnKp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]
[Fur,+] 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
nd Fur-Fe2+ activator glnKp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]
[Fur,-] 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
nd Fur-Fe2+ repressor glnKp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]
[GadX,+] 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
nd GadX activator glnKp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [4]
[NtrC,+] 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 NtrC-phosphorylated activator glnKp 472461 472477 -87.0 taacgcactgTGCACTGTCATAGTGCGttttcatttt nd [COMP-HINF-SIMILAR-TO-CONSENSUS] nd [1]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

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

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

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

 [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] van Heeswijk WC., Hoving S., Molenaar D., Stegeman B., Kahn D., Westerhoff HV., 1996, An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli., Mol Microbiol 21(1):133-46

 [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] Reitzer L., Schneider BL., 2001, Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli., Microbiol Mol Biol Rev 65(3):422-44, table of contents

 [4] Hommais F., Krin E., Coppee JY., Lacroix C., Yeramian E., Danchin A., Bertin P., 2004, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli., Microbiology 150(Pt 1):61-72

 [5] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3

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