RegulonDB RegulonDB 10.6.3: 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 |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]|.
EnvZ-OmpR positively controls MicF RNA under high-osmolarity conditions |CITS:[7519595]|, SoxS under oxidative stress |CITS:[7679383]|, and MarA in response to antibiotic stress |CITS:[2848006]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
[LTED] Length of transcript experimentally determined
Reference(s): [1] Andersen J., et al., 1987
Promoter
Name: micFp
+1: 2313084
Sigma Factor: Sigma38, Sigma70
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]
[TIM]
Reference(s): [1] Andersen J., et al., 1987
[2] Seo SW., et al., 2015
TF binding sites (TFBSs)
[AcrR,-] Phrase
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 atttattaccGTCATTCATTTCTGAATGTCTGTTtacccctatt nd [AIBSCS] [14]
[H-NS,-] Phrase
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 [GEA] [8], [18]
[HU,+] Phrase
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 [GEA] [17]
[IHF,-] Phrase
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 tcaaggttaaAATCAATAACTTAttcttaagta nd [BCE], [BPP], [GEA], [HIBSCS] [11]
[Lrp,-] Phrase
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 attaactttaTTTATTACCGTCATTcatttctgaa nd [BPP], [GEA] [8], [15], [16]
remote Lrp repressor micFp 2313134 2313148 58.5 tgaatgtctgTTTACCCCTATTTCAaccggatgcc nd [BPP], [GEA] [8], [15], [16]
remote Lrp repressor micFp 2313163 2313177 87.5 gatgcctcgcATTCGGTTTTTTTTAcccttcttta nd [BPP], [GEA] [8], [15], [16]
remote Lrp-leucine repressor micFp 2313199 2313210 122.0 acacttttcaTTATTCTGTGCTaccacagaaa nd [BPP], [GEA] [8], [16]
[MarA,+] Phrase
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 aagtatttgaCAGCACTGAATGTCAAAACAaaaccttcac nd [AIBSCS], [BPP], [GEA], [HIBSCS] [8], [12], [13], [14]
[OmpR,+] Phrase
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 atccaacacgAATATGATACTAAAACTTTTaagatgtttc nd [BPP], [GEA], [HIBSCS], [SM] [3], [4], [5], [6]
remote OmpR-P activator micFp 2312888 2312907 -186.5 taaaacttttAAGATGTTTCATTTATCGCTatagatgttt nd [BPP], [GEA], [HIBSCS], [SM] [3], [4], [6], [7]
remote OmpR-P activator micFp 2312909 2312928 -165.5 tttatcgctaTAGATGTTTCAAAATGTAAAtgcaagggaa nd [BPP], [GEA], [HIBSCS], [SM] [3], [4], [6], [7]
[Rob,+] Phrase
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 aagtatttgaCAGCACTGAATGTCAAAACAaaaccttcac nd [BPP], [GEA], [HIBSCS] [12]
[SoxS,+] Phrase
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 aagattattgCGGAATGGCGAAATAAGCACctaacatcaa nd [BCE], [BPP], , [IHBCE], [8], [9], [10]
proximal SoxS activator micFp 2313036 2313055 -38.5 gtatttgacaGCACTGAATGTCAAAACAAAaccttcactc nd [BCE], [BPP], , [IHBCE], [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.


Evidence    

 [HIPP] Human inference of promoter position

 [TIM] Transcription initiation mapping

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [GEA] Gene expression analysis

 [BCE] Binding of cellular extracts

 [BPP] Binding of purified proteins

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation

 [CEUMA] ChIP-exo evidence used in manual assertion

 [IHBCE] Inferred by a human based on computational evidence

 [RE] RNA-seq evidence


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] 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

 [3] 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

 [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] 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

 [15] 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

 [16] 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

 [17] 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

 [18] 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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