RegulonDB RegulonDB 11.2: 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
The transition from low to high expression of the sufABCDSE operon is regulated via the burst size of transcription but not by the burst frequency of transcription, as observed for operons transcribed from σ54 promoters Engl C,2020.
By using ChIP-Seq analysis, it was observed that the protein PdeL binds upstream of the gene sufA Sellner B,2021.
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
[IC-ADJ-GENES-SAME-BIO-PROCESS] 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: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [4] Huerta AM., et al., 2003
[5] 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 Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fur-Fe2+ repressor sufAp 1764427 1764445 -18.0 gggttgaactGATAATCATTATCACTAACatgctgttat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5], [6], [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 sufAp 1764557 1764569 -145.0 taataaccatTATCTAACAATGAgatacctaat nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5]
[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
proximal IscR activator sufAp 1764448 1764472 -42.5 ttttacggtaAAGCCCCTGCGTTTGCTGGGTTGAActgataatca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IMP], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [5], [6], [7], [10], [13]
remote IscR activator sufAp 1764510 1764534 -104.5 ttagcgtgccTGTTAACCCACACATCAGGGTCTATgcttattaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6], [7], [10]
remote IscR activator sufAp 1764551 1764575 -145.5 cttagataatAACCATTATCTAACAATGAGATACCtaattcttag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6], [7], [10]
[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 sufAp 1764419 1764430 -6.0 tcattatcacTAACATGCTGTTatacgctgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [11], [12]
proximal NsrR repressor sufAp 1764481 1764492 -68.0 aaaagcaggcAAAAAGCATGTTttacggtaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [11], [12]
[OxyR,+] 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 OxyR activator sufAp 1764620 1764636 -210.0 ctatctcttaAATAGTCATTTTCAATAcaactttttc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [5], [6], [7], [8], [10]
remote OxyR activator sufAp 1764642 1764658 -232.0 tctgaacgctGCACTTTTTTACCTATCtcttaaatag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO], [EXP-CHIP-SEQ-MANUAL], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [3], [5], [6], [7], [8], [9], [10]


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-IMP] Inferred from mutant phenotype

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

 [EXP-IMP-SITE-MUTATION] Site mutation

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

 [EXP-IEP-RNA-SEQ] high throughput RNA-seq evidence

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

 [EXP-CHIP-EXO] high throughput ChIP-exo evidence

 [EXP-CHIP-SEQ-MANUAL] ChIP-seq evidence used in manual assertion


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] 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] 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

 [6] Engl C., Jovanovic G., Brackston RD., Kotta-Loizou I., Buck M., 2020, The route to transcription initiation determines the mode of transcriptional bursting in E. coli., Nat Commun 11(1):2422

 [7] 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

 [8] 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

 [9] 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

 [10] 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

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

 [12] 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

 [13] 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

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