RegulonDB RegulonDB 10.10: Operon Form
   

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




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


Transcription unit          
Name: sodB
Gene(s): sodB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The proteins Fur and HNS regulate the transcription of the sodB gene; although a Fur-binding site has been identified in the regulatory region of sodB, the regulation of the two regulators appears to be indirect Dubrac S, Touati D,2002 Transcriptional fusion experiments demonstrated a positive effect of Fur and a negative effect of HNS on sodB transcription Dubrac S, Touati D,2002. Niederhoffer EC,1990. Zhang Z,2005 and gel shift assays have shown a weak interaction between Fur and the regulatory region of sodB Dubrac S, Touati D,2002. Niederhoffer EC,1990 However, an in vitro transcription analysis demonstrated that Fur has no direct effect on the transcription of sodB Dubrac S, Touati D,2002 It should be noted that Fur regulates in a negative way RhyB, a small RNA that negatively regulates the expression of sodB Masse E,2002 On the other hand, the effect of HNS on the sodB promoter depends on the presence of Fur; in addition, no curved DNA region was identified to bind HNS around the promoter region of sodB Dubrac S, Touati D,2002
Promoter
Name: sodBp
+1: 1735323
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 55
Sequence: ttgttacggcaacagggtaagttcatcttttgtctcaccttttaatttgctaccctatccAtacgcacaataaggctattg
                              -35                  -10      +1                   
Note(s): This promoter is member of the extended -10 class of promoters.
The TSS in sodBp identified by Liu et al. (2018) using Capping-RACE differs by 2 bp from that identified by Carlioz et al. (1988) and Dubrac et al. (2000) Liu F,2018
Evidence: [HTTIM]
[ICWHO]
[IMP]
[TIM]
Reference(s): [1] Carlioz A., et al., 1988
[2] Dubrac S., et al., 2000
[3] Huerta AM., et al., 2003
[4] Liu F., et al., 2018
Terminator(s)
Type: rho-independent
Sequence: ttgtcagcaaCTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTgtttaattag
Reference(s): [1] Carlioz A., et al., 1988
TF binding sites (TFBSs)
[CRP,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote CRP-cyclic-AMP repressor sodBp 1735376 1735398 64.5 aggagagtagCAATGTCATTCGAATTACCTGCActaccatatg nd [GEA], [AIBSCS] [12]
[IHF,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF repressor sodBp 1735256 1735268 -61.0 gctaaaacttTACCCTGTTGTTAcggcaacagg nd [GEA], [AIBSCS] [2]
[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 sodBp 1735281 1735292 -37.0 gcaacagggtAAGTTCATCTTTtgtctcacct nd [GEA], [AIBSCS] [11]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA RyhB sodB repressor 1735365 1735382 AAGGAGAGUAGCAAUGUC TRANSLATION-BLOCKING, MRNA-DEGRADATION [IEP], [IPI], [SM] [5], [6], [7], [8]
small regulatory RNA FnrS sodB repressor 1735340 1735397 AUUGUACGUAUGCAAAUUAAUAAUAAAGGAGAGUAGCAAUGUCAUUCGAAUUACCUGC nd [IDA], [IEP], [SM] [9], [10]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [13] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -18.8 1735251 1735295 cttcgctaaaACTTTACCCTGTTGTTACGGCAACAGGGTAAGTTCATCTTTTGTctcacctttt
  anti-terminator -4.53 1735222 1735260 gcgctcgtcgGGTAATGACCCCAAAAACACTTCGCTAAAACTTTACCCtgttgttacg
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    

 [HTTIM] High-throughput transcription initiation mapping

 [ICWHO] Inferred computationally without human oversight

 [IMP] Inferred from mutant phenotype

 [TIM] Transcription initiation mapping

 [GEA] Gene expression analysis

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [IEP] Inferred from expression pattern

 [IPI] Inferred from physical interaction

 [SM] Site mutation

 [IDA] Inferred from direct assay


Reference(s)    

 [1] Carlioz A., Ludwig ML., Stallings WC., Fee JA., Steinman HM., Touati D., 1988, Iron superoxide dismutase. Nucleotide sequence of the gene from Escherichia coli K12 and correlations with crystal structures., J Biol Chem 263(3):1555-62

 [2] Dubrac S., Touati D., 2000, Fur positive regulation of iron superoxide dismutase in Escherichia coli: functional analysis of the sodB promoter., J Bacteriol 182(13):3802-8

 [3] 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

 [4] Liu F., Zheng K., Chen HC., Liu ZF., 2018, Capping-RACE: a simple, accurate, and sensitive 5' RACE method for use in prokaryotes., Nucleic Acids Res 46(21):e129

 [5] Afonyushkin T., Vecerek B., Moll I., Blasi U., Kaberdin VR., 2005, Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB., Nucleic Acids Res 33(5):1678-89

 [6] Prevost K., Desnoyers G., Jacques JF., Lavoie F., Masse E., 2011, Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage., Genes Dev 25(4):385-96

 [7] Urban JH., Vogel J., 2007, Translational control and target recognition by Escherichia coli small RNAs in vivo., Nucleic Acids Res 35(3):1018-37

 [8] Vecerek B., Moll I., Afonyushkin T., Kaberdin V., Blasi U., 2003, Interaction of the RNA chaperone Hfq with mRNAs: direct and indirect roles of Hfq in iron metabolism of Escherichia coli., Mol Microbiol 50(3):897-909

 [9] Boysen A., Moller-Jensen J., Kallipolitis B., Valentin-Hansen P., Overgaard M., 2010, Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli., J Biol Chem 285(14):10690-702

 [10] Durand S., Storz G., 2010, Reprogramming of anaerobic metabolism by the FnrS small RNA., Mol Microbiol 75(5):1215-31

 [11] 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

 [12] Zhang Z., Gosset G., Barabote R., Gonzalez CS., Cuevas WA., Saier MH., 2005, Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli., J Bacteriol 187(3):980-90

 [13] Merino E, Yanofsky C., 2005, Transcription attenuation: a highly conserved regulatory strategy used by bacteria., Trends Genet. 2005 May;21(5):260-4.

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