RegulonDB RegulonDB 11.1: 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
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for nirB . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
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: [COMP-AINF]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [3] Browning DF., et al., 2008
[1] Harborne NR., et al., 1992
[4] Huerta AM., et al., 2003
[5] Jayaraman PS., et al., 1987
[6] Salgado H, et al., 2012
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
remote CRP-cyclic-AMP repressor nirBp 3493680 3493701 -296.5 acgctgtcgtCTTTGTGATGTGCTTCCTGTTAggtttcgtca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
proximal CRP-cyclic-AMP repressor nirBp 3493935 3493956 -41.5 atataaaggtGAATTTGATTTACATCAATAAGcggggttgct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
[Cra,-] 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 Cra repressor nirBp 3493963 3493980 -15.5 taagcggggtTGCTGAATCGTTAAGGTAggcggtaata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [8], [16]
[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 activator nirBp 3493939 3493952 -41.5 aaaggtgaatTTGATTTACATCAAtaagcggggt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [8], [13], [14], [15]
[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
remote Fis repressor nirBp 3493838 3493852 -142.0 cgctcattttGTCTATTTTTTGCACaaacatgaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [8], [9]
remote Fis repressor nirBp 3493883 3493897 -97.0 ttccgtgactTAAGAAAATTTATACaaatcagcaa nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [8]
proximal Fis repressor nirBp 3494002 3494016 23.0 aaaagaaatcGAGGCAAAAATGAGCaaagtcagac nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [8], [10]
[H-NS,-] 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 H-NS repressor nirBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [8], [10]
[IHF,+] 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
remote IHF activator nirBp 3493866 3493878 -115.0 catgaaatatCAGACAATTCCGTgacttaagaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [8]
[IHF,-] 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 IHF repressor nirBp 3493893 3493905 -88.0 taagaaaattTATACAAATCAGCaatataccca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [8], [10]
[NarL,+] 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 NarL-phosphorylated activator nirBp 3493910 3493916 -74.0 atcagcaataTACCCATtaaggagtat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [11], [12]
proximal NarL-phosphorylated activator nirBp 3493919 3493925 -65.0 atacccattaAGGAGTAtataaaggtg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [11], [12]
[NarP,+] 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 NarP-phosphorylated activator nirBp 3493905 3493920 -74.0 tacaaatcagCAATATACCCATTAAGgagtatataa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [11], [12]
proximal NarP-phosphorylated activator nirBp 3493914 3493929 -65.0 gcaatataccCATTAAGGAGTATATAaaggtgaatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [8], [11], [12]


Transcription unit       
Name: cysG
Gene(s): cysG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] 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: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-RNA-POLYMERASE-FOOTPRINTING]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [17] Belyaeva T., et al., 1993
[4] Huerta AM., et al., 2003
[2] Peakman T., et al., 1990


Transcription unit       
Name: cysG
Gene(s): cysG   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] 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: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [17] 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"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [EXP-IDA] Inferred from direct assay

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

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

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

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

 [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-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

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

 [EXP-IMP-SITE-MUTATION] Site mutation

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

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

 [EXP-IMP] Inferred from mutant phenotype


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] 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

 [4] 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

 [5] 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

 [6] 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.

 [7] 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

 [8] 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

 [9] 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

 [10] 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

 [11] 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

 [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 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

 [16] 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

 [17] 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

 [18] Wright PR., Richter AS., Papenfort K., Mann M., Vogel J., Hess WR., Backofen R., Georg J., 2013, Comparative genomics boosts target prediction for bacterial small RNAs., Proc Natl Acad Sci U S A 110(37):E3487-96

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