RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: nrdHIEF
Synonym(s): nrdEF
Gene(s): nrdH, nrdI, nrdE, nrdF   Genome Browser M3D Gene expression COLOMBOS
Note(s): nrdHIEF is induced under H2O2 stress conditions (oxidative stress) Martin JE,2011
Fur, NrdR, and IscR control nrdHIEF expression independently of one another Martin JE,2011
An increase in the expression of nrdH has been observed when CysB is highly overexpressed Liu H,2020.
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Jordan A., et al., 1996
Promoter
Name: nrdHp
+1: 2800656
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 67
Sequence: ccactatttgctatatattgtgtggttgaatcttttttcaactacatctagtatctctgtAtcaacagagagacaacccga
                          -35                    -10        +1                   
Note(s): A σ32-dependent promoter was suggested to be located upstream of nrdH Wade JT,2006, but it is unknown whether this promoter is the same as nrdHp.
Evidence: [COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Jordan A., et al., 1996
TF binding sites (TFBSs)
[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
proximal Fur-Fe2+ repressor nrdHp 2800586 2800604 -61.0 catatccaggGTAATTTCGACCACTATTTgctatatatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [3]
[IscR,+] 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 IscR activator nrdHp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2]
[NrdR,-] 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 NrdR-Zn2+ repressor nrdHp 2800603 2800618 -45.5 cgaccactatTTGCTATATATTGTGTggttgaatct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
proximal NrdR-Zn2+ repressor nrdHp 2800634 2800649 -14.5 aatcttttttCAACTACATCTAGTATctctgtatca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -15.6 2800505 2800537 cgcgtctttgACCCCGAAGCCTGTCTTCGGGGTTTCTTTTTGcctggtgaat
  anti-terminator -4.7 2800470 2800512 atgcgcaaatCGTAGTGCAAAAATGATAATAAATACGCGTCTTTGACCCCGAagcctgtctt
  anti-anti-terminator -11.04 2800435 2800478 ctgcggtaggTATTTTTATCGGCGCACTGTTAAGCATGCGCAAATCGTAGTGCaaaaatgata
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-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

 [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-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Jordan A., Aragall E., Gibert I., Barbe J., 1996, Promoter identification and expression analysis of Salmonella typhimurium and Escherichia coli nrdEF operons encoding one of two class I ribonucleotide reductases present in both bacteria., Mol Microbiol 19(4):777-90

 [2] Martin JE., Imlay JA., 2011, The alternative aerobic ribonucleotide reductase of Escherichia coli, NrdEF, is a manganese-dependent enzyme that enables cell replication during periods of iron starvation., Mol Microbiol 80(2):319-34

 [3] Vassinova N., Kozyrev D., 2000, A method for direct cloning of fur-regulated genes: identification of seven new fur-regulated loci in Escherichia coli., Microbiology 146 Pt 12:3171-3182

 [4] Torrents E., Grinberg I., Gorovitz-Harris B., Lundstrom H., Borovok I., Aharonowitz Y., Sjoberg BM., Cohen G., 2007, NrdR controls differential expression of the Escherichia coli ribonucleotide reductase genes., J Bacteriol 189(14):5012-21

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