RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit       
Name: nikABCDER
Gene(s): nikA, nikB, nikC, nikD, nikE, nikR   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] De Pina K., et al., 1999
[2] Eitinger T., et al., 2000
[3] Navarro C., et al., 1993
Promoter
Name: nikAp2
+1: 3613439
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 228
Sequence: agccatcgttaaacagcgtggcggcagcgcctggcaaatcgtcagcgtagacagcacctaTcactcctcgctgtcagtcag
                                -24         -12             +1                   
Note(s): This promoter was identified by microarray and ChIP assays with a mutant
σ54 strain and a σ54-overexpressing strain,
and by σ54-related promoter element identification Zhao K,2010
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-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
Reference(s): [4] Huerta AM., et al., 2003
[5] Zhao K., et al., 2010


Transcription unit          
Name: nikABCDER
Gene(s): nikA, nikB, nikC, nikD, nikE, nikR   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of the proteins involved in nickel transport (NikABCDE) are essential for hydrogenase activity Rowe JL,2005
Evidence: [EXP-IEP] Inferred from expression pattern
[EXP-IEP-COREGULATION] Inferred through co-regulation
[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s): [1] De Pina K., et al., 1999
[2] Eitinger T., et al., 2000
[3] Navarro C., et al., 1993
Promoter
Name: nikAp1
+1: 3613628
Distance from start of the gene: 39
Sequence: gactgcccatctattgatccagaacaggtaatcagtatgacgaatacttaaaatcgtcatActtatttccgccatctattt
Evidence: [COMP-HINF-POSITIONAL-IDENTIFICATION]
Reference(s): [6] Chivers PT., et al., 2000
[3] Navarro C., et al., 1993
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 activator nikAp1 3613581 3613595 -40.5 tgcccatctaTTGATCCAGAACAGGtaatcagtat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IMP-SITE-MUTATION] C [3], [7]
[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
nd NarL-phosphorylated repressor nikAp1 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [9]
[NikR,-] 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 NikR-Ni2+ repressor nikAp1 3613602 3613630 -12.5 caggtaatcaGTATGACGAATACTTAAAATCGTCATACTtatttccgcc nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [6], [7], [8]


Transcription unit       
Name: nikR
Gene(s): nikR   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: nikRp
+1: 3618537
Distance from start of the gene: 51
Sequence: ggtggtgggagagaaattaaccttttcctctgacgccggacgtgtgctacaaaacgcggtAttacccgcattccccgtgcg
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [1] De Pina K., et al., 1999
[10] Salgado H, et al., 2012


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -9.9 3613602 3613635 aggtaatcagTATGACGAATACTTAAAATCGTCATACTTATTTccgccatcta
  anti-terminator -5.2 3613577 3613607 gactgcccatCTATTGATCCAGAACAGGTAATCAGTATGAcgaatactta
  anti-anti-terminator -11.3 3613536 3613588 agtgtgcaatGGATCGATTCAGTTAACTGATCCGCCCACCCGACTGCCCATCTATTGATCCAgaacaggtaa
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

 [COMP-HINF] Inferred by a human based on computational evidence

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

 [EXP-IEP] Inferred from expression pattern

 [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.

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence

 [EXP-IMP-SITE-MUTATION] Site mutation

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

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

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


Reference(s)    

 [1] De Pina K., Desjardin V., Mandrand-Berthelot MA., Giordano G., Wu LF., 1999, Isolation and characterization of the nikR gene encoding a nickel-responsive regulator in Escherichia coli., J Bacteriol 181(2):670-4

 [2] Eitinger T., Mandrand-Berthelot MA., 2000, Nickel transport systems in microorganisms., Arch Microbiol 173(1):1-9

 [3] Navarro C., Wu LF., Mandrand-Berthelot MA., 1993, The nik operon of Escherichia coli encodes a periplasmic binding-protein-dependent transport system for nickel., Mol Microbiol 9(6):1181-91

 [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] Zhao K., Liu M., Burgess RR., 2010, Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis., Nucleic Acids Res 38(4):1273-83

 [6] Chivers PT., Sauer RT., 2000, Regulation of high affinity nickel uptake in bacteria. Ni2+-Dependent interaction of NikR with wild-type and mutant operator sites., J Biol Chem 275(26):19735-41

 [7] Chivers PT., Sauer RT., 1999, NikR is a ribbon-helix-helix DNA-binding protein., Protein Sci 8(11):2494-500

 [8] Krecisz S., Jones MD., Zamble DB., 2012, Nonspecific interactions between Escherichia coli NikR and DNA are critical for nickel-activated DNA binding., Biochemistry 51(40):7873-9

 [9] Rowe JL., Starnes GL., Chivers PT., 2005, Complex transcriptional control links NikABCDE-dependent nickel transport with hydrogenase expression in Escherichia coli., J Bacteriol 187(18):6317-23

 [10] 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.

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