RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: sufABCDSE
Synonym(s): suf
Gene(s): sufE, sufS, sufD, sufC, sufB, sufA   Genome Browser M3D Gene expression COLOMBOS
Note(s): OxyR, IHF, and an unidentified oxidant-responsive factor are involved in the oxidant induction of the suf operon Lee JH,2004.
IscR regulates in a coordinated manner the expression of the iscRSUA to the sufABCDSE operons through repression by [2Fe-2S]-IscR and activation by apo-IscR, respectively. Both the apo- and holoprotein conformations were able to activate the Suf pathway in order to maintain differential control for Fe-S cluster biogenesis pathways to ensure viability under a variety of growth conditions Mettert EL,2014
The accumulation of the proteins encoded in the sufABCDSE operon and the accumulation of its activator IscR are enhanced during iron-limiting conditions Zupok A,2019.
NsrR is a regulator of the sufA promoter and contributes to its upregulation upon exposure to NO Chhabra S,2015
Evidence: [ITC] Inferred through co-regulation
[PAGTSBP] Products of adjacent genes in the same biological process
Reference(s): [1] Patzer SI., et al., 1999
[2] Takahashi Y., et al., 2002
[3] Zheng M., et al., 2001
Promoter
Name: sufAp
+1: 1764418
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 32
Sequence: acggtaaagcccctgcgtttgctgggttgaactgataatcattatcactaacatgctgttAtacgctgaaagcgatgaagt
                           -35                   -10        +1                   
Note(s): The transcriptional activity of this promoter is induced by hydrogen peroxide and superoxide generators, such as paraquat, menadione, plumbagin and phenazine metho-sulfate Lee JH,2004.
Evidence: [HIPP]
[IMP]
[TIM]
Reference(s): [4] Lee JH., et al., 2004
[2] Takahashi Y., et al., 2002
[3] Zheng M., et al., 2001
TF binding sites (TFBSs)
[Fur,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fur-Fe2+ repressor sufAp 1764427 1764445 -18.0 gggttgaactGATAATCATTATCACTAACatgctgttat nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [SM] [2], [4], [6], [8], [12]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF1 activator sufAp 1764557 1764569 -145.0 taataaccatTATCTAACAATGAgatacctaat nd [BPP], [CV(SM)], [SM] [4], [6]
[IscR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IscR activator sufAp 1764448 1764472 -42.5 ttttacggtaAAGCCCCTGCGTTTGCTGGGTTGAActgataatca nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [CV(GEA/SM)], [CV(SM)], [GEA], [IMP], [SM] [4], [5], [8], [11], [12]
remote IscR activator sufAp 1764510 1764534 -104.5 ttagcgtgccTGTTAACCCACACATCAGGGTCTATgcttattaaa nd [BPP], [GEA] [5], [8]
remote IscR activator sufAp 1764551 1764575 -145.5 cttagataatAACCATTATCTAACAATGAGATACCtaattcttag nd [BPP], [GEA] [5], [8]
[NsrR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NsrR repressor sufAp 1764419 1764430 -6.0 tcattatcacTAACATGCTGTTatacgctgaa nd [APIORCISFBSCS], [CV(GEA)], [GEA] [9], [10]
proximal NsrR repressor sufAp 1764481 1764492 -68.0 aaaagcaggcAAAAAGCATGTTttacggtaaa nd [APIORCISFBSCS], [CV(GEA)], [GEA] [9], [10]
[OxyR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote OxyR activator sufAp 1764620 1764636 -210.0 ctatctcttaAATAGTCATTTTCAATAcaactttttc nd [BPP], [CV(SM)], [GEA], [SM] [3], [4], [5], [6], [8]
remote OxyR activator sufAp 1764642 1764658 -232.0 tctgaacgctGCACTTTTTTACCTATCtcttaaatag nd [BPP], , [CV(GEA)], [CV(GEA)], [GEA], [IHBCE], [3], [4], [5], [6], [7], [8]
Note(s): 1It is suggested that IHF bends the DNA to facilitate the interaction between OxyR and the promoter-bound complex Lee JH,2004.
4It is suggested that IHF bends the DNA to facilitate the interaction between OxyR and the promoter-bound complex Lee JH,2004.


Evidence    

 [HIPP] Human inference of promoter position

 [IMP] Inferred from mutant phenotype

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [CV(GEA/SM)] cross validation(GEA/SM)

 [CV(SM)] cross validation(SM)

 [GEA] Gene expression analysis

 [SM] Site mutation

 [CEUMA] ChIP-seq evidence used in manual assertion

 [IHBCE] Inferred by a human based on computational evidence

 [RE] RNA-seq evidence


Reference(s)    

 [1] Patzer SI., Hantke K., 1999, SufS is a NifS-like protein, and SufD is necessary for stability of the [2Fe-2S] FhuF protein in Escherichia coli., J Bacteriol 181(10):3307-9

 [2] Takahashi Y., Tokumoto U., 2002, A third bacterial system for the assembly of iron-sulfur clusters with homologs in archaea and plastids., J Biol Chem 277(32):28380-3

 [3] Zheng M., Wang X., Templeton LJ., Smulski DR., LaRossa RA., Storz G., 2001, DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide., J Bacteriol 183(15):4562-70

 [4] Lee JH., Yeo WS., Roe JH., 2004, Induction of the sufA operon encoding Fe-S assembly proteins by superoxide generators and hydrogen peroxide: involvement of OxyR, IHF and an unidentified oxidant-responsive factor., Mol Microbiol 51(6):1745-55

 [5] Jang S., Imlay JA., 2010, Hydrogen peroxide inactivates the Escherichia coli Isc iron-sulphur assembly system, and OxyR induces the Suf system to compensate., Mol Microbiol 78(6):1448-67

 [6] Outten FW., Djaman O., Storz G., 2004, A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli., Mol Microbiol 52(3):861-72

 [7] Seo SW., Kim D., Szubin R., Palsson BO., 2015, Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655., Cell Rep 12(8):1289-99

 [8] Yeo WS., Lee JH., Lee KC., Roe JH., 2006, IscR acts as an activator in response to oxidative stress for the suf operon encoding Fe-S assembly proteins., Mol Microbiol 61(1):206-18

 [9] Chhabra S., Spiro S., 2015, Inefficient translation of nsrR constrains behaviour of the NsrR regulon in Escherichia coli., Microbiology 161(10):2029-38

 [10] 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

 [11] Giel JL., Rodionov D., Liu M., Blattner FR., Kiley PJ., 2006, IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O-regulated genes in Escherichia coli., Mol Microbiol 60(4):1058-75

 [12] Mettert EL., Kiley PJ., 2014, Coordinate regulation of the Suf and Isc Fe-S cluster biogenesis pathways by IscR is essential for viability of Escherichia coli., J Bacteriol 196(24):4315-23

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