RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: hmp
Gene(s): hmp   Genome Browser M3D Gene expression COLOMBOS
Note(s): Membrillo et al. in 1998 showed that MetR at low concentrations activates the hmp gene, when it binds to the binding site located at -80 Membrillo-Hernandez J,1998, and simultaneously represses transcription of the glyA gene Membrillo-Hernandez J,1998. In addition, they showed that homocysteine did not alter the levels of transcription of this gene and that S-nitrosoglutathione and sodium nitroprusside increase transcription of the hmp gene in the presence of MetR.
Based on gene expression analysis, it was shown that CsgD could be a negative regulator of hmp expression Herrington MB,2013
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Membrillo-Hernandez J., et al., 1997
[2] Plamann MD., et al., 1983
Promoter
Name: hmpp
+1: 2685797
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 38
Sequence: tttctgaaaaacaccaaagaaccatttacattgcagggctattttttataagatgcatttGagatacatcaattaagatgc
                         -35              -10               +1                   
Note(s): Hydrogen peroxide (H2O2) and nitric oxide (NO) stresses suppress the transcript output of the hmpp promoter, even in the absence of NsrR; however, prioritized detoxification depends on both NsrR and Hmp Adolfsen KJ, Chou WK, Brynildsen MP,2019
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[1] Membrillo-Hernandez J., et al., 1997
[2] Plamann MD., et al., 1983
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
proximal FNR repressor hmpp 2685795 2685808 5.5 taagatgcatTTGAGATACATCAAttaagatgca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [10], [11]
[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
proximal Fur-Fe2+ repressor hmpp 2685793 2685811 6.0 tataagatgcATTTGAGATACATCAATTAagatgcaaaa nd [AS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP], [AS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [12], [13], [14]
[MetR,+] 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 MetR activator hmpp 2685710 2685724 -80.0 caggtttgtgATGCAAATTTTTCACttcatcacat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5], [6], [7]
[NsrR,-] 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 NsrR repressor hmpp 2685754 2685765 -38.0 aaaacaccaaAGAACCATTTACattgcagggc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [8]
proximal NsrR repressor hmpp 2685789 2685807 2.0 tttttataagATGCATTTGAGATACATCAattaagatgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9]
proximal NsrR repressor hmpp 2685811 2685822 20.0 tacatcaattAAGATGCAAAAAaaggaagacc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [8]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA SdsN hmp repressor 2685841 2685846 GACGCU nd [EXP-IMP-SITE-MUTATION] [4]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation hmpp nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [1]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [1] Membrillo-Hernandez J., et al., 1997


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [EXP-IDA-RNA-POLYMERASE-FOOTPRINTING] RNA polymerase footprinting

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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [AS] Author statement

 [EXP-IMP] Inferred from mutant phenotype

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


Reference(s)    

 [1] Membrillo-Hernandez J., Cook GM., Poole RK., 1997, Roles of RpoS (sigmaS), IHF and ppGpp in the expression of the hmp gene encoding the flavohemoglobin (Hmp) of Escherichia coli K-12., Mol Gen Genet 254(5):599-603

 [2] Plamann MD., Stauffer GV., 1983, Characterization of the Escherichia coli gene for serine hydroxymethyltransferase., Gene 22(1):9-18

 [3] 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

 [4] Hao Y., Updegrove TB., Livingston NN., Storz G., 2016, Protection against deleterious nitrogen compounds: role of σS-dependent small RNAs encoded adjacent to sdiA., Nucleic Acids Res 44(14):6935-48

 [5] Lorenz E., Stauffer GV., 1995, Characterization of the MetR binding sites for the glyA gene of Escherichia coli., J Bacteriol 177(14):4113-20

 [6] Lorenz E., Stauffer GV., 1996, MetR-mediated repression of the glyA gene in Escherichia coli., FEMS Microbiol Lett 144(2-3):229-33

 [7] Membrillo-Hernandez J., Coopamah MD., Channa A., Hughes MN., Poole RK., 1998, A novel mechanism for upregulation of the Escherichia coli K-12 hmp (flavohaemoglobin) gene by the 'NO releaser', S-nitrosoglutathione: nitrosation of homocysteine and modulation of MetR binding to the glyA-hmp intergenic region., Mol Microbiol 29(4):1101-12

 [8] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

 [9] Bodenmiller DM., Spiro S., 2006, The yjeB (nsrR) gene of Escherichia coli encodes a nitric oxide-sensitive transcriptional regulator., J Bacteriol 188(3):874-81

 [10] Cruz-Ramos H., Crack J., Wu G., Hughes MN., Scott C., Thomson AJ., Green J., Poole RK., 2002, NO sensing by FNR: regulation of the Escherichia coli NO-detoxifying flavohaemoglobin, Hmp., EMBO J 21(13):3235-44

 [11] Poole RK., Anjum MF., Membrillo-Hernandez J., Kim SO., Hughes MN., Stewart V., 1996, Nitric oxide, nitrite, and Fnr regulation of hmp (flavohemoglobin) gene expression in Escherichia coli K-12., J Bacteriol 178(18):5487-92

 [12] Crawford MJ., Goldberg DE., 1998, Regulation of the Salmonella typhimurium flavohemoglobin gene. A new pathway for bacterial gene expression in response to nitric oxide., J Biol Chem 273(51):34028-32

 [13] D'Autreaux B., Touati D., Bersch B., Latour JM., Michaud-Soret I., 2002, Direct inhibition by nitric oxide of the transcriptional ferric uptake regulation protein via nitrosylation of the iron., Proc Natl Acad Sci U S A 99(26):16619-24

 [14] Hernandez-Urzua E., Zamorano-Sanchez DS., Ponce-Coria J., Morett E., Grogan S., Poole RK., Membrillo-Hernandez J., 2007, Multiple regulators of the Flavohaemoglobin (hmp) gene of Salmonella enterica serovar Typhimurium include RamA, a transcriptional regulator conferring the multidrug resistance phenotype., Arch Microbiol 187(1):67-77

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