RegulonDB RegulonDB 10.8: Operon Form
   

nirBDC-cysG operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: nirBDC-cysG
Synonym(s): OP00062, nirB, nirBDC
Gene(s): nirB, nirD, nirC, cysG   Genome Browser M3D Gene expression COLOMBOS
Note(s): Effects of IHF and Fis in the nirBDC-cysG are position dependent, i.e., both transcriptional regulators must be correctly positioned to be regulated pnir Browning DF,2008
The IHF II (-115) site functions independently of IHF I (-88) and Fis I (-142). Both transcriptional regulators repress transcription initiation by interfering with RNA polymerase binding Browning DF,2008
Fis represses transcription in the absence of IHF I and IHF II, and this repression is less efficient when one or both of the DNA sites for IHF are inactivated Browning DF,2008
Reference(s): [1] Harborne NR., et al., 1992
[2] Peakman T., et al., 1990
Promoter
Name: nirBp
+1: 3493987
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 24
Sequence: ataaaggtgaatttgatttacatcaataagcggggttgctgaatcgttaaggtaggcggtAatagaaaagaaatcgaggca
                      -35                       -10         +1                   
Note(s): Nitrate causes repression of the nirBp promoter in a NarL protein-dependent way, while the repression of the same promoter by nitrite is dependent on the NarL protein or the NarP protein Stewart V,2003
Evidence: [CV(RS-EPT-CBR)]
[CV(TIM)]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Harborne NR., et al., 1992
[3] Jayaraman PS., et al., 1987
[4] Salgado H, et al., 2012
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cAMP repressor nirBp 3493680 3493701 -296.5 acgctgtcgtCTTTGTGATGTGCTTCCTGTTAggtttcgtca nd [AIBSCS], [CV(GEA)], [GEA] [5]
proximal CRP-cAMP repressor nirBp 3493935 3493956 -41.5 atataaaggtGAATTTGATTTACATCAATAAGcggggttgct nd [AIBSCS], [CV(GEA)], [GEA] [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Cra1 repressor nirBp 3493963 3493980 -15.5 taagcggggtTGCTGAATCGTTAAGGTAggcggtaata nd [APIORCISFBSCS], [BCE], [CV(GEA)], [GEA] [6], [15]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal FNR1 activator nirBp 3493939 3493952 -41.5 aaaggtgaatTTGATTTACATCAAtaagcggggt nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [6], [7], [11], [13], [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis1 repressor nirBp 3493838 3493852 -142.0 cgctcattttGTCTATTTTTTGCACaaacatgaaa nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [6], [7], [8]
remote Fis2 repressor nirBp 3493883 3493897 -97.0 ttccgtgactTAAGAAAATTTATACaaatcagcaa nd [APIORCISFBSCS], [BPP] [6]
proximal Fis3 repressor nirBp 3494002 3494016 23.0 aaaagaaatcGAGGCAAAAATGAGCaaagtcagac nd [AIBSCS], [BPP] [6], [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS1 repressor nirBp nd nd nd nd nd [BPP], [GEA] [6], [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF1 activator nirBp 3493866 3493878 -115.0 catgaaatatCAGACAATTCCGTgacttaagaa nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [6], [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF1 repressor nirBp 3493893 3493905 -88.0 taagaaaattTATACAAATCAGCaatataccca nd [BCE], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [6], [7], [9]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarL-Phosphorylated activator nirBp 3493905 3493920 -74.0 tacaaatcagCAATATACCCATTAAGgagtatataa nd [BCE], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [6], [10], [11], [12]
proximal NarL-Phosphorylated2 activator nirBp 3493914 3493929 -65.0 gcaatataccCATTAAGGAGTATATAaaggtgaatt nd [BCE], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [6], [10], [11], [12]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NarP-Phosphorylated activator nirBp 3493905 3493920 -74.0 tacaaatcagCAATATACCCATTAAGgagtatataa nd [BCE], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [6], [10], [11], [12]
proximal NarP-Phosphorylated2 activator nirBp 3493914 3493929 -65.0 gcaatataccCATTAAGGAGTATATAaaggtgaatt nd [BCE], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [6], [10], [11], [12]
Note(s): 1FruR represses the nirB operon in the absence of glucose binding to its promoter. It is suggested that Cra probably interferes with RNA polymerase binding to its site or with the RNA polymerase interaction with FNR and other components for transcription initiation.1The nir promoter is 100% dependent on FNR. If there is no FNR, there is no activity. This activity can be efficiently repressed by FruR (-16.5 site) and less efficiently by HNS and Fis (+23 site). FNR-dependent activation of the nir promoter is repressed by IHF (-88 site) and Fis (-142 site), DNA-binding proteins that play a role in shaping the folded bacterial chromosome. Although Fis and IHF repress FNR-dependent activation of the nir promoter, they do not prevent FNR binding. Thus, Fis, IHF, and FNR can bind simultaneously.1Although Fis and IHF repress FNR-dependent activation of the nir promoter, they do not prevent FNR binding. Thus, Fis, IHF, and FNR can bind simultaneously.
2The effect of Fis (-97 site) in the local nucleoprotein structure is not yet clear.
3Fis binds to this site and represses efficiently (less than FruR) the activity of FNR (-41.5 site) in the nir promoter.1Hns binds to this site and represses efficiently (less than FruR) the activity of FNR (-41.5 site) in the nir promoter.1IHF (-115 site) increases FNR-dependent activation by decreasing the repression mediated by IHF (-88 site) and Fis (-142 site). It is a weak site.1Although Fis and IHF repress FNR-dependent activation of the nir promoter, they do not prevent FNR binding. Thus, Fis, IHF, andFNR can bind simultaneously.2The maximum nirB expression is achieved at high nitrate concentrations through the proteins NarL and NarP, which function independently of each other, but NarL appears to be the main activator. The nitrite is a less effective inductor of nirB expression Wang H,2000.
NarL counteracts the repressive effect of IHF (-88 site) and Fis (-142 site). This site interferes with the binding of IHF (-88 site). However, IHF cannot displace prebound NarL. Browning et al. Browning DF,2004 suggested that NarL interferes with IHF (-88 binding site) at the nir promoter by distorting the minor groove at its target site, and they argued that the resulting activation by NarL results from remodeling of the local nucleoprotein structure to facilitate FNR-dependent transcription.2NarP appears to antagonize the activation of nirB by NarL at low nitrate concentrations, but not when nitrite is present Wang H,2000.2Although Fis and IHF repress FNR-dependent activation of the nir promoter, they do not prevent FNR binding. Thus, Fis, IHF, and FNR can bind simultaneously.
3IHF (-115 site) increases FNR-dependent activation by decreasing the repression mediated by IHF (-88 site) and Fis (-142 site). It is a weak site.
4The effect of Fis (-97 site) in the local nucleoprotein structure is not yet clear.
5Although Fis and IHF repress FNR-dependent activation of the nir promoter, they do not prevent FNR binding. Thus, Fis, IHF, andFNR can bind simultaneously.
8NarP appears to antagonize the activation of nirB by NarL at low nitrate concentrations, but not when nitrite is present Wang H,2000.
9The maximum nirB expression is achieved at high nitrate concentrations through the proteins NarL and NarP, which function independently of each other, but NarL appears to be the main activator. The nitrite is a less effective inductor of nirB expression Wang H,2000.
NarL counteracts the repressive effect of IHF (-88 site) and Fis (-142 site). This site interferes with the binding of IHF (-88 site). However, IHF cannot displace prebound NarL. Browning et al. Browning DF,2004 suggested that NarL interferes with IHF (-88 binding site) at the nir promoter by distorting the minor groove at its target site, and they argued that the resulting activation by NarL results from remodeling of the local nucleoprotein structure to facilitate FNR-dependent transcription.
10The nir promoter is 100% dependent on FNR. If there is no FNR, there is no activity. This activity can be efficiently repressed by FruR (-16.5 site) and less efficiently by HNS and Fis (+23 site). FNR-dependent activation of the nir promoter is repressed by IHF (-88 site) and Fis (-142 site), DNA-binding proteins that play a role in shaping the folded bacterial chromosome. Although Fis and IHF repress FNR-dependent activation of the nir promoter, they do not prevent FNR binding. Thus, Fis, IHF, and FNR can bind simultaneously.
12FruR represses the nirB operon in the absence of glucose binding to its promoter. It is suggested that Cra probably interferes with RNA polymerase binding to its site or with the RNA polymerase interaction with FNR and other components for transcription initiation.
13Fis binds to this site and represses efficiently (less than FruR) the activity of FNR (-41.5 site) in the nir promoter.
14Hns binds to this site and represses efficiently (less than FruR) the activity of FNR (-41.5 site) in the nir promoter.


Transcription unit       
Name: cysG
Gene(s): cysG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [2] Peakman T., et al., 1990
Promoter
Name: cysGp1
+1: 3497754
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 74
Sequence: tgggtaatactttatcaggtgccgtattcatgggattgggttattggtatgctacgccgaAagcgaatcgtccggttgcgg
                           -35                  -10         +1                   
Evidence: [CV(RPF)]
[CV(RPF/TIM)]
[CV(TIM)]
[HIPP]
[IMP]
[RPF]
[TIM]
Reference(s): [16] Belyaeva T., et al., 1993
[2] Peakman T., et al., 1990


Transcription unit       
Name: cysG
Gene(s): cysG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [2] Peakman T., et al., 1990
Promoter
Name: cysGp2
+1: 3497793
Distance from start of the gene: 35
Sequence: gttattggtatgctacgccgaaagcgaatcgtccggttgcggacaaatttaatcaaactgAaacggctgccggttaattac
Evidence: [TIM]
Reference(s): [16] Belyaeva T., et al., 1993
[2] Peakman T., et al., 1990


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -13.5 3496917 3496956 ttttgcatggTCCTGTAATAATCTTCGGTATATTGCAGGACATTTTTTAaactttttgt
  anti-terminator -19.2 3496872 3496920 cagctgcgcgGTTAATGTTTTAACGGGAGGCGCAATGCCTCCCCTTTTTGCATGGTCCtgtaataatc
  anti-anti-terminator -16.2 3496839 3496895 cattacgaagCGCGAGTGAAAGACGGCGTGGTGCAGCTGCGCGGTTAATGTTTTAACGGGAGGCGCaatgcctccc
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"




Reference(s)    

 [1] Harborne NR., Griffiths L., Busby SJ., Cole JA., 1992, Transcriptional control, translation and function of the products of the five open reading frames of the Escherichia coli nir operon., Mol Microbiol 6(19):2805-13

 [2] Peakman T., Busby S., Cole J., 1990, Transcriptional control of the cysG gene of Escherichia coli K-12 during aerobic and anaerobic growth., Eur J Biochem 191(2):325-31

 [3] Jayaraman PS., Peakman TC., Busby SJ., Quincey RV., Cole JA., 1987, Location and sequence of the promoter of the gene for the NADH-dependent nitrite reductase of Escherichia coli and its regulation by oxygen, the Fnr protein and nitrite., J Mol Biol 196(4):781-8

 [4] 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.

 [5] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [6] Browning DF., Cole JA., Busby SJ., 2004, Transcription activation by remodelling of a nucleoprotein assembly: the role of NarL at the FNR-dependent Escherichia coli nir promoter., Mol Microbiol 53(1):203-15

 [7] Browning DF., Cole JA., Busby SJ., 2008, Regulation by nucleoid-associated proteins at the Escherichia coli nir operon promoter., J Bacteriol 190(21):7258-67

 [8] Wu H., Tyson KL., Cole JA., Busby SJ., 1998, Regulation of transcription initiation at the Escherichia coli nir operon promoter: a new mechanism to account for co-dependence on two transcription factors., Mol Microbiol 27(2):493-505

 [9] Browning DF., Cole JA., Busby SJ., 2000, Suppression of FNR-dependent transcription activation at the Escherichia coli nir promoter by Fis, IHF and H-NS: modulation of transcription initiation by a complex nucleo-protein assembly., Mol Microbiol 37(5):1258-69

 [10] Darwin AJ., Tyson KL., Busby SJ., Stewart V., 1997, Differential regulation by the homologous response regulators NarL and NarP of Escherichia coli K-12 depends on DNA binding site arrangement., Mol Microbiol 25(3):583-95

 [11] Tyson KL., Bell AI., Cole JA., Busby SJ., 1993, Definition of nitrite and nitrate response elements at the anaerobically inducible Escherichia coli nirB promoter: interactions between FNR and NarL., Mol Microbiol 7(1):151-7

 [12] Wang H., Gunsalus RP., 2000, The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite., J Bacteriol 182(20):5813-22

 [13] Eiglmeier K., Honore N., Iuchi S., Lin EC., Cole ST., 1989, Molecular genetic analysis of FNR-dependent promoters., Mol Microbiol 3(7):869-78

 [14] Jayaraman PS., Gaston KL., Cole JA., Busby SJ., 1988, The nirB promoter of Escherichia coli: location of nucleotide sequences essential for regulation by oxygen, the FNR protein and nitrite., Mol Microbiol 2(4):527-30

 [15] Tyson K., Busby S., Cole J., 1997, Catabolite regulation of two Escherichia coli operons encoding nitrite reductases: role of the Cra protein., Arch Microbiol 168(3):240-4

 [16] Belyaeva T., Griffiths L., Minchin S., Cole J., Busby S., 1993, The Escherichia coli cysG promoter belongs to the 'extended -10' class of bacterial promoters., Biochem J 296 ( Pt 3):851-7


RegulonDB