RegulonDB RegulonDB 9.4: Operon Form

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

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 |CITS:[8002608]|.
The expression of the micF gene is affected by antibiotic pressure |CITS:[17426813]|. An increase in the micF expression is maintained during exposure to increasing concentrations of the antibiotic tetracycline |CITS:[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 |CITS:[17426813]|.
Salicylate activates the inaAp and micFp promoters through Rob |CITS:[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 |CITS:[ 23497217]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Andersen J., et al., 1987
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]
Reference(s): [1] Andersen J., et al., 1987
TF binding sites (TFBSs)
Transcription factor Function Promoter Binding Sites Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
OmpR-Phosphorylated activator micFp 2312868 2312887 -206.5 atccaacacgAATATGATACTAAAACTTTTaagatgtttc [BPP], [GEA], [HIBSCS], [SM] [2], [3], [4], [5]
OmpR-Phosphorylated activator micFp 2312888 2312907 -186.5 taaaacttttAAGATGTTTCATTTATCGCTatagatgttt [BPP], [GEA], [HIBSCS], [SM] [2], [3], [5], [6]
OmpR-Phosphorylated activator micFp 2312909 2312928 -165.5 tttatcgctaTAGATGTTTCAAAATGTAAAtgcaagggaa [BPP], [GEA], [HIBSCS], [SM] [2], [3], [5], [6]
SoxS activator micFp 2312955 2312974 -119.5 aagattattgCGGAATGGCGAAATAAGCACctaacatcaa [BCE], [BPP] [7], [8]
IHF5 repressor micFp 2313006 2313018 -72.0 tcaaggttaaAATCAATAACTTAttcttaagta [BCE], [BPP], [GEA], [HIBSCS] [9]
Rob activator micFp 2313034 2313053 -40.0 aagtatttgaCAGCACTGAATGTCAAAACAaaaccttcac [BPP], [GEA], [HIBSCS] [10]
MarA activator micFp 2313034 2313053 -40.0 aagtatttgaCAGCACTGAATGTCAAAACAaaaccttcac [AIBSCS], [BPP], [GEA], [HIBSCS] [7], [10], [11], [12]
SoxS activator micFp 2313036 2313055 -38.5 gtatttgacaGCACTGAATGTCAAAACAAAaccttcactc [BCE], [BPP] [7], [8]
Lrp repressor micFp 2313103 2313117 27.5 attaactttaTTTATTACCGTCATTcatttctgaa [BPP], [GEA] [7], [13], [14]
AcrR repressor micFp 2313112 2313135 41.0 atttattaccGTCATTCATTTCTGAATGTCTGTTtacccctatt [AIBSCS] [12]
Lrp repressor micFp 2313134 2313148 58.5 tgaatgtctgTTTACCCCTATTTCAaccggatgcc [BPP], [GEA] [7], [13], [14]
Lrp repressor micFp 2313163 2313177 87.5 gatgcctcgcATTCGGTTTTTTTTAcccttcttta [BPP], [GEA] [7], [13], [14]
Lrp-Leucine repressor micFp 2313199 2313210 122.0 acacttttcaTTATTCTGTGCTaccacagaaa [BPP], [GEA] [7], [14]
HU activator micFp nd nd nd nd [GEA] [15]
H-NS repressor micFp nd nd nd nd [GEA] [7], [16]
Note(s): 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.


 [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] Coyer J., Andersen J., Forst SA., Inouye M., Delihas N., 1990, micF RNA in ompB mutants of Escherichia coli: different pathways regulate micF RNA levels in response to osmolarity and temperature change., J Bacteriol. 172(8):4143-50

 [3] 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

 [4] 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

 [5] 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

 [6] 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

 [7] 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

 [8] 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

 [9] 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

 [10] 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

 [11] 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

 [12] 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

 [13] Ernsting BR., Atkinson MR., Ninfa AJ., Matthews RG., 1992, Characterization of the regulon controlled by the leucine-responsive regulatory protein in Escherichia coli., J Bacteriol. 174(4):1109-18

 [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] 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

 [16] 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