RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: ndh
Synonym(s): OP00217
Gene(s): ndh   Genome Browser M3D Gene expression COLOMBOS
Note(s): NDH-2 activity and ndh expression are maintained during the stationary phase in the presence of phosphate under aerobic conditions. This regulation is independent of RpoS and the phoR-phoB system, and it perhaps is regulated by systems and mechanisms not yet described Schurig-Briccio LA, Rintoul MR, Volentini SI, Farías RN, Baldomà L, Badía J, Rodríguez-Montelongo L, Rapisarda VA,2008
During anaerobiosis or aerobiosis, Fis binds to -72 and -123 sites and activates transcription of the ndh promoter at low concentrations but represses transcription at higher concentrations, when it is also bound to the +51 site. The -72 Fis site is the major activator of ndh expression Jackson L,2004. Under appropriate growth conditions, both FNR and Fis may bind simultaneously to the upstream region of the ndh promoter.
The expression of the ndh gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB Kumar R,2011
Based on kinetic modeling, PdhR was identified as the source of the asymmetry in the ndh transcript profile during aerobic-to-anaerobic and anaerobic-to-aerobic transitions Rolfe MD,2012.
In 2012, Rolfe et al. showed that ArcA repressed the transcription of the ndh gene Rolfe MD,2012. This result is consistent with the locations of the predicted ArcA-binding sites proposed by Liu et al. in 2004: one binding site upstream of the transcription start site at -57 and five binding sites downstream at +36, +52, +57, +66, and +68 Liu X,2004 In addition, the results obtained by Liu et al. in 2004 came from microarray analyses, and those authors did not specify the regulated promoter Liu X,2004. To date, only one transcription start site has been identified in this intergenic region, and it is possible that ArcA acts positively on another unidentified promoter or has an indirect effect.
The transcript of ndh is increased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
Reference(s): [1] Green J., et al., 1994
Promoter
Name: ndhp
+1: 1165992
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 93
Sequence: aacttgattaacatcaattttggtatgaccaatgcaccattcatgttattctcaatagcgAagaacattttcattgctgta
                    -35                        -10          +1                   
Note(s): Like pdhRp, ndhp and cyoAp are repressed by PdhR and derepressed by the addition of pyruvate Ogasawara H,2007
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Huerta AM., et al., 2003
[3] Sharrocks AD., et al., 1991
TF binding sites (TFBSs)
[ArcA,-] 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 ArcA-phosphorylated repressor ndhp 1165928 1165942 -57.0 cttttcagcaACAAAACTTGATTAAcatcaatttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9], [10]
remote ArcA-phosphorylated repressor ndhp 1166020 1166034 36.0 gtaacctgttGTTAATTAAGAGCTAtgttaataac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9], [10]
remote ArcA-phosphorylated repressor ndhp 1166036 1166050 52.0 taagagctatGTTAATAACCATTAAttaacaattg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9], [10]
remote ArcA-phosphorylated repressor ndhp 1166041 1166055 57.0 gctatgttaaTAACCATTAATTAACaattggttaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9], [10]
remote ArcA-phosphorylated repressor ndhp 1166050 1166064 66.0 ataaccattaATTAACAATTGGTTAataaatttaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9], [10]
remote ArcA-phosphorylated repressor ndhp 1166052 1166066 68.0 aaccattaatTAACAATTGGTTAATaaatttaagg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [9], [10]
[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
remote FNR repressor ndhp 1165891 1165904 -94.5 actctgttttTTGATCTCACCCGGtaaagtcgcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [5], [6], [7]
proximal FNR repressor ndhp 1165935 1165948 -50.5 gcaacaaaacTTGATTAACATCAAttttggtatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IMP-SITE-MUTATION] C [5], [6], [7]
[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 activator ndhp 1165862 1165876 -123.0 cacaaattcgCTCAAATAATAAACAataaactctg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [5]
proximal Fis activator ndhp 1165913 1165927 -72.0 ggtaaagtcgCCTATCTTTTCAGCAacaaaacttg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-EXO], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [5]
[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 ndhp 1166035 1166049 51.0 ttaagagctaTGTTAATAACCATTAattaacaatt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [5]
[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
nd Fur-Fe2+ repressor ndhp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [6]
[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 ndhp 1165928 1165940 -58.0 cttttcagcaACAAAACTTGATTaacatcaatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [8]
proximal IHF repressor ndhp 1165969 1165981 -17.0 accaatgcacCATTCATGTTATTctcaatagcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [8]
proximal IHF repressor ndhp 1166011 1166023 26.0 ttcattgctgTAACCTGTTGTTAattaagagct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [8]
[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 ndhp 1165992 1166003 6.0 ctcaatagcgAAGAACATTTTCattgctgtaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [13]
[PdhR,-] 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 PdhR repressor ndhp 1165949 1165965 -35.0 ttaacatcaaTTTTGGTATGACCAATGcaccattcat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [11], [12]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

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

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

 [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-EXO] high throughput ChIP-exo evidence

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

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

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence


Reference(s)    

 [1] Green J., Guest JR., 1994, Regulation of transcription at the ndh promoter of Escherichia coli by FNR and novel factors., Mol Microbiol 12(3):433-44

 [2] 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

 [3] Sharrocks AD., Green J., Guest JR., 1991, FNR activates and represses transcription in vitro., Proc R Soc Lond B Biol Sci 245(1314):219-26

 [4] Green J., Anjum MF., Guest JR., 1996, The ndh-binding protein (Nbp) regulates the ndh gene of Escherichia coli in response to growth phase and is identical to Fis., Mol Microbiol 20(5):1043-55

 [5] Jackson L., Blake T., Green J., 2004, Regulation of ndh expression in Escherichia coli by Fis., Microbiology 150(Pt 2):407-13

 [6] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3

 [7] Salmon K., Hung SP., Mekjian K., Baldi P., Hatfield GW., Gunsalus RP., 2003, Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR., J Biol Chem 278(32):29837-55

 [8] Green J., Anjum MF., Guest JR., 1997, Regulation of the ndh gene of Escherichia coli by integration host factor and a novel regulator, Arr., Microbiology 143 ( Pt 9):2865-75

 [9] Liu X., De Wulf P., 2004, Probing the ArcA-P modulon of Escherichia coli by whole genome transcriptional analysis and sequence recognition profiling., J Biol Chem 279(13):12588-97

 [10] Rolfe MD., Ocone A., Stapleton MR., Hall S., Trotter EW., Poole RK., Sanguinetti G., Green J., 2012, Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations., Open Biol 2(7):120091

 [11] Anzai T., Imamura S., Ishihama A., Shimada T., 2020, Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility., Microb Genom 6(10)

 [12] Ogasawara H., Ishida Y., Yamada K., Yamamoto K., Ishihama A., 2007, PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli., J Bacteriol 189(15):5534-41

 [13] 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

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