RegulonDB RegulonDB 10.8: 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: [AISDTU] Automated inference that a single-gene directon is a transcription unit
[BTEI] 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 31061166
Evidence: [CV(RPF/TA)]
[CV(RPF/TIM)]
[CV(TA/TIM)]
[HIPP]
[RPF]
[TIM]
Reference(s): [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 (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR1 repressor hmpp 2685795 2685808 5.5 taagatgcatTTGAGATACATCAAttaagatgca nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [1], [10], [11]
[Fur,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fur-Fe2+ repressor hmpp 2685793 2685811 6.0 tataagatgcATTTGAGATACATCAATTAagatgcaaaa nd [APIORCISFBSCS], [AS], [CV(GEA/ROMA)], [GEA], [IMP] [12], [13], [14]
[MetR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MetR activator hmpp 2685710 2685724 -80.0 caggtttgtgATGCAAATTTTTCACttcatcacat nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [IMP], [SM] [3], [4], [5], [6], [7]
[NsrR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NsrR repressor hmpp 2685754 2685765 -38.0 aaaacaccaaAGAACCATTTACattgcagggc nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [8]
proximal NsrR repressor hmpp 2685789 2685807 2.0 tttttataagATGCATTTGAGATACATCAattaagatgc nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [9]
proximal NsrR repressor hmpp 2685811 2685822 20.0 tacatcaattAAGATGCAAAAAaaggaagacc nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [8]
Note(s): 1Nitric oxide (NO) inactivates the FNR protein, so NO induces hmpA expression .4Nitric oxide (NO) inactivates the FNR protein, so NO induces hmpA expression .
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation hmpp   [GEA] [1]
Evidence: [GEA] Gene expression analysis
Reference(s): [1] Membrillo-Hernandez J., et al., 1997


Evidence    

 [CV(RPF/TA)] cross validation(RPF/TA)

 [CV(RPF/TIM)] cross validation(RPF/TIM)

 [CV(TA/TIM)] cross validation(TA/TIM)

 [HIPP] Human inference of promoter position

 [RPF] RNA polymerase footprinting

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)

 [CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)

 [GEA] Gene expression analysis

 [SM] Site mutation

 [AS] Author statement

 [IMP] Inferred from mutant phenotype

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

 [4] Lorenz E., Stauffer GV., 1996, RNA polymerase, PurR and MetR interactions at the glyA promoter of Escherichia coli., Microbiology 142 ( Pt 7):1819-24

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

 [6] Lorenz E., Stauffer GV., 1996, Cooperative MetR binding in the Escherichia coli glyA control region., FEMS Microbiol Lett 137(2-3):147-52

 [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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