RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit          
Name: micF
Gene(s): micF   Genome Browser M3D Gene expression COLOMBOS
Note(s): The regulation of micF by Lrp indirectly affects the regulation of ompF (a porin), as micF codes for the antisense RNA that inhibits ompF translation Ferrario M,1995
The expression of the micF gene is affected by antibiotic pressure 17426813 An increase in the micF expression is maintained during exposure to increasing concentrations of the antibiotic tetracycline 17426813 In the same experiment, an increase of micF expression correlated with the expression of the marA gene, which codes for an activator of micF 17426813
Salicylate activates the inaAp and micFp promoters through Rob 22753060
The transcription of the gene micF is enhanced under high oxygen saturation (300%) in the absence of the superoxide dismutase proteins SodA and SodB Baez A,2013
EnvZ-OmpR positively controls MicF RNA under high-osmolarity conditions 7519595 SoxS under oxidative stress 7679383 and MarA in response to antibiotic stress 2848006
The RNA produced by the micF gene has been observed mainly in the poles of the cell during stress conditions 31540875.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Andersen J., et al., 1987
Promoter
Name: micFp
+1: 2313084
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 0
Sequence: aagtatttgacagcactgaatgtcaaaacaaaaccttcactcgcaactagaataactcccGctatcatcattaactttatt
                      -35                       -10         +1                   
Note(s): The micFp promoter is situated within the micF structural gene, which controls a new species of micF RNA (4.5 S). The micF gene encodes a nontranslated 93-nt antisense RNA (6 S).
Evidence: [HIPP]
[ICWHO]
[TIM]
Reference(s): [1] Andersen J., et al., 1987
[2] Huerta AM., et al., 2003
[3] Seo SW., et al., 2015
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote AcrR repressor micFp 2313112 2313135 41.0 atttattaccGTCATTCATTTCTGAATGTCTGTTTacccctattt nd [AIBSCS] [15]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor micFp nd nd nd nd nd [BPP], [GEA], [IGI] [8], [17]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd HU activator micFp nd nd nd nd nd [BPP], [GEA], [IGI] [16]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF1 repressor micFp 2313006 2313018 -72.0 tcaaggttaaAATCAATAACTTATtcttaagtat nd [APIORCISFBSCS], [BCE], [BPP], [GEA] [11]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Lrp repressor micFp 2313103 2313117 27.5 attaactttaTTTATTACCGTCATTCatttctgaat nd [BPP], [GEA] [8], [14]
remote Lrp repressor micFp 2313134 2313148 58.5 tgaatgtctgTTTACCCCTATTTCAAccggatgcct nd [BPP], [GEA] [8], [14]
remote Lrp repressor micFp 2313163 2313177 87.5 gatgcctcgcATTCGGTTTTTTTTACccttctttac nd [BPP], [GEA] [8], [14]
remote Lrp-leucine repressor micFp 2313199 2313210 122.0 acacttttcaTTATTCTGTGCTAccacagaaaa nd [BPP], [GEA] [8], [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MarA activator micFp 2313034 2313053 -40.0 aagtatttgaCAGCACTGAATGTCAAAACAAaaccttcact nd [APIORCISFBSCS], [BPP], [GEA] [8], [13]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote OmpR-P activator micFp 2312868 2312887 -206.5 atccaacacgAATATGATACTAAAACTTTTAagatgtttca nd [APIORCISFBSCS], [BPP], [GEA], [SM] [4], [5], [6]
remote OmpR-P activator micFp 2312888 2312907 -186.5 taaaacttttAAGATGTTTCATTTATCGCTAtagatgtttc nd [APIORCISFBSCS], [BPP], [GEA], [SM] [4], [6], [7]
remote OmpR-P activator micFp 2312909 2312928 -165.5 tttatcgctaTAGATGTTTCAAAATGTAAATgcaagggaac nd [APIORCISFBSCS], [BPP], [GEA], [SM] [4], [6], [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Rob activator micFp 2313034 2313053 -40.0 aagtatttgaCAGCACTGAATGTCAAAACAAaaccttcact nd [APIORCISFBSCS], [BPP], [GEA] [12]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote SoxS activator micFp 2312955 2312974 -119.5 aagattattgCGGAATGGCGAAATAAGCACCtaacatcaag nd [BCE], [BPP], [CEEUMA], [IHBCE], [RSE] [8], [9], [10]
proximal SoxS activator micFp 2313036 2313055 -38.5 gtatttgacaGCACTGAATGTCAAAACAAAAccttcactcg nd [BCE], [BPP], [CEEUMA], [IHBCE], [RSE] [8], [9], [10]
Note(s): 1The regulatory effect of IHF on the promoter micFp1 is not yet known. However, we have assigned a negative effect to this regulatory interaction based on the fact that the protein's binding site overlaps the transcription start site of the promoter.5The regulatory effect of IHF on the promoter micFp1 is not yet known. However, we have assigned a negative effect to this regulatory interaction based on the fact that the protein's binding site overlaps the transcription start site of the promoter.


Transcription unit          
Name: micF
Gene(s): micF   Genome Browser M3D Gene expression COLOMBOS
Note(s): The regulation of micF by Lrp indirectly affects the regulation of ompF (a porin), as micF codes for the antisense RNA that inhibits ompF translation Ferrario M,1995
The expression of the micF gene is affected by antibiotic pressure 17426813 An increase in the micF expression is maintained during exposure to increasing concentrations of the antibiotic tetracycline 17426813 In the same experiment, an increase of micF expression correlated with the expression of the marA gene, which codes for an activator of micF 17426813
Salicylate activates the inaAp and micFp promoters through Rob 22753060
The transcription of the gene micF is enhanced under high oxygen saturation (300%) in the absence of the superoxide dismutase proteins SodA and SodB Baez A,2013
EnvZ-OmpR positively controls MicF RNA under high-osmolarity conditions 7519595 SoxS under oxidative stress 7679383 and MarA in response to antibiotic stress 2848006
The RNA produced by the micF gene has been observed mainly in the poles of the cell during stress conditions 31540875.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Andersen J., et al., 1987
Promoter
Name: micFp2
+1: 2313084
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 0
Sequence: aagtatttgacagcactgaatgtcaaaacaaaaccttcactcgcaactagaataactcccGctatcatcattaactttatt
Note(s): The micFp promoter is situated within the micF structural gene, which controls a new species of micF RNA (4.5 S). The micF gene encodes a nontranslated 93-nt antisense RNA (6 S).
Evidence: [HIPP]
[TIM]
Reference(s): [1] Andersen J., et al., 1987
[3] Seo SW., et al., 2015
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote AcrR repressor micFp2 2313112 2313135 41.0 atttattaccGTCATTCATTTCTGAATGTCTGTTTacccctattt nd [AIBSCS] [15]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd H-NS repressor micFp2 nd nd nd nd nd [BPP], [GEA], [IGI] [8], [17]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd HU activator micFp2 nd nd nd nd nd [BPP], [GEA], [IGI] [16]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF1 repressor micFp2 2313006 2313018 -72.0 tcaaggttaaAATCAATAACTTATtcttaagtat nd [APIORCISFBSCS], [BCE], [BPP], [GEA] [11]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Lrp repressor micFp2 2313103 2313117 27.5 attaactttaTTTATTACCGTCATTCatttctgaat nd [BPP], [GEA] [8], [14]
remote Lrp repressor micFp2 2313134 2313148 58.5 tgaatgtctgTTTACCCCTATTTCAAccggatgcct nd [BPP], [GEA] [8], [14]
remote Lrp repressor micFp2 2313163 2313177 87.5 gatgcctcgcATTCGGTTTTTTTTACccttctttac nd [BPP], [GEA] [8], [14]
remote Lrp-leucine repressor micFp2 2313199 2313210 122.0 acacttttcaTTATTCTGTGCTAccacagaaaa nd [BPP], [GEA] [8], [14]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MarA activator micFp2 2313034 2313053 -40.0 aagtatttgaCAGCACTGAATGTCAAAACAAaaccttcact nd [APIORCISFBSCS], [BPP], [GEA] [8], [13]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote OmpR-P activator micFp2 2312868 2312887 -206.5 atccaacacgAATATGATACTAAAACTTTTAagatgtttca nd [APIORCISFBSCS], [BPP], [GEA], [SM] [4], [5], [6]
remote OmpR-P activator micFp2 2312888 2312907 -186.5 taaaacttttAAGATGTTTCATTTATCGCTAtagatgtttc nd [APIORCISFBSCS], [BPP], [GEA], [SM] [4], [6], [7]
remote OmpR-P activator micFp2 2312909 2312928 -165.5 tttatcgctaTAGATGTTTCAAAATGTAAATgcaagggaac nd [APIORCISFBSCS], [BPP], [GEA], [SM] [4], [6], [7]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Rob activator micFp2 2313034 2313053 -40.0 aagtatttgaCAGCACTGAATGTCAAAACAAaaccttcact nd [APIORCISFBSCS], [BPP], [GEA] [12]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote SoxS activator micFp2 2312955 2312974 -119.5 aagattattgCGGAATGGCGAAATAAGCACCtaacatcaag nd [BCE], [BPP], [CEEUMA], [IHBCE], [RSE] [8], [9], [10]
proximal SoxS activator micFp2 2313036 2313055 -38.5 gtatttgacaGCACTGAATGTCAAAACAAAAccttcactcg nd [BCE], [BPP], [CEEUMA], [IHBCE], [RSE] [8], [9], [10]
Note(s): 1The regulatory effect of IHF on the promoter micFp1 is not yet known. However, we have assigned a negative effect to this regulatory interaction based on the fact that the protein's binding site overlaps the transcription start site of the promoter.5The regulatory effect of IHF on the promoter micFp1 is not yet known. However, we have assigned a negative effect to this regulatory interaction based on the fact that the protein's binding site overlaps the transcription start site of the promoter.




Reference(s)    

 [1] Andersen J., Delihas N., Ikenaka K., Green PJ., Pines O., Ilercil O., Inouye M., 1987, The isolation and characterization of RNA coded by the micF gene in Escherichia coli., Nucleic Acids Res 15(5):2089-101

 [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] Seo SW., Kim D., O'Brien EJ., Szubin R., Palsson BO., 2015, Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli., Nat Commun 6:7970

 [4] Mattison K., Oropeza R., Byers N., Kenney LJ., 2002, A phosphorylation site mutant of OmpR reveals different binding conformations at ompF and ompC., J Mol Biol 315(4):497-511

 [5] Qin L., Yoshida T., Inouye M., 2001, The critical role of DNA in the equilibrium between OmpR and phosphorylated OmpR mediated by EnvZ in Escherichia coli., Proc Natl Acad Sci U S A 98(3):908-13

 [6] Yoshida T., Qin L., Egger LA., Inouye M., 2006, Transcription regulation of ompF and ompC by a single transcription factor, OmpR., J Biol Chem 281(25):17114-23

 [7] Tsung K., Brissette RE., Inouye M., 1989, Identification of the DNA-binding domain of the OmpR protein required for transcriptional activation of the ompF and ompC genes of Escherichia coli by in vivo DNA footprinting., J Biol Chem 264(17):10104-9

 [8] Delihas N., Forst S., 2001, MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors., J Mol Biol 313(1):1-12

 [9] Li Z., Demple B., 1994, SoxS, an activator of superoxide stress genes in Escherichia coli. Purification and interaction with DNA., J Biol Chem 269(28):18371-7

 [10] 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

 [11] Huang L., Tsui P., Freundlich M., 1990, Integration host factor is a negative effector of in vivo and in vitro expression of ompC in Escherichia coli., J Bacteriol 172(9):5293-8

 [12] Kwon HJ., Bennik MH., Demple B., Ellenberger T., 2000, Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA., Nat Struct Biol 7(5):424-30

 [13] Gillette WK., Martin RG., Rosner JL., 2000, Probing the Escherichia coli transcriptional activator MarA using alanine-scanning mutagenesis: residues important for DNA binding and activation., J Mol Biol 299(5):1245-55

 [14] Ferrario M., Ernsting BR., Borst DW., Wiese DE., Blumenthal RM., Matthews RG., 1995, The leucine-responsive regulatory protein of Escherichia coli negatively regulates transcription of ompC and micF and positively regulates translation of ompF., J Bacteriol 177(1):103-13

 [15] Rodionov DA., Gelfand MS., Mironov AA., Rakhmaninova AB., 2001, Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria., J Mol Microbiol Biotechnol 3(2):319-24

 [16] Painbeni E., Caroff M., Rouviere-Yaniv J., 1997, Alterations of the outer membrane composition in Escherichia coli lacking the histone-like protein HU., Proc Natl Acad Sci U S A 94(13):6712-7

 [17] Deighan P., Free A., Dorman CJ., 2000, A role for the Escherichia coli H-NS-like protein StpA in OmpF porin expression through modulation of micF RNA stability., Mol Microbiol 38(1):126-39


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