RegulonDB RegulonDB 10.9: Gene Form
   

micF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rcsD ompC micF ompC3\' Lrp Lrp CpxR Lrp Lrp AcrR Lrp SoxS Rob MarA Lrp IHF CpxR SoxS CpxR OmpR OmpR YjjQ OmpR Lrp Lrp Lrp Lrp Lrp Lrp MicC RybB RseX anti-anti-terminator anti-terminator TSS_2489 (cluster) TSS_2489 (cluster) rcsBp2 rcsBp2 rcsBp1 rcsBp1 rcsDp rcsDp micFp micFp ompCp3 ompCp3 ompCp2 ompCp2 ompCp1 ompCp1 TSS_2488 TSS_2488 TSS_2487 TSS_2487 TSS_2486 TSS_2486 TSS_2485 TSS_2485 TSS_2484 TSS_2484

Gene      
Name: micF    Texpresso search in the literature
Synonym(s): ECK2208, EG30063, b4439, stc
Genome position(nucleotides): 2313084 --> 2313176 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 35.48
External database links:  
ASAP:
 ABE-0047259
CGSC:
 18157
ECHOBASE:
 EB4226
ECOLIHUB:
 micF
COLOMBOS: micF


Product      
Name: small regulatory RNA MicF
Synonym(s): MicF, Stc
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.7 - antisense RNA
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.1 - translation attenuation and efficiency
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.6 - antisense RNA
  5 - cell processes --> 5.10 - defense/survival
  5 - cell processes --> 5.5 - adaptations
  5 - cell processes --> 5.6 - protection --> 5.6.4 - drug resistance/sensitivity
Gene Ontology Terms (GO)  
molecular_function GO:0000900 - translation repressor activity, mRNA regulatory element binding
GO:0005515 - protein binding
GO:0003729 - mRNA binding
GO:0048027 - mRNA 5'-UTR binding
biological_process GO:0006979 - response to oxidative stress
GO:0042493 - response to drug
GO:0040033 - negative regulation of translation, ncRNA-mediated
GO:0034605 - cellular response to heat
GO:0071474 - cellular hyperosmotic response
Note(s): Note(s): ...[more].
Evidence: [IDA] Inferred from direct assay
[IE] Inferred from experiment
Reference(s): [1] Andersen J., et al., 1989
[2] Chen S., et al., 2002
[3] Delihas N. 1997
[4] Komatsu T., et al., 1990
[5] Kumar A., et al., 2016
[6] Mihailovic MK., et al., 2018
[7] Tkachenko AG., et al., 2006
[8] Urban JH., et al., 2007
[9] Vogt SL., et al., 2014
[10] Zhang C., et al., 2020
External database links:  
ECOCYC:
 MICF-RNA
ECOLIWIKI:
 b4439


Operon      
Name: micF         
Operon arrangement:
Transcription unit        Promoter
micF
micF


Transcriptional Regulation      
Display Regulation             
Activated by: MarA, OmpR, Rob, HU, SoxS
Repressed by: H-NS, IHF, Lrp, AcrR
Growth Conditions:

[1] 

C: Escherichia coli| protox assay
E: Escherichia coli| chenodeoxycholate; protox assay

[2] 

C: Escherichia coli| protox assay
E: Escherichia coli| protox assay; ursodeoxycholate

[3] 

C: Escherichia coli| protox assay
E: Escherichia coli| glycocholate; protox assay

[4] 

C: Escherichia coli| protox assay
E: Escherichia coli| deoxycholate; protox assay


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_2484 2311836 reverse nd [RS-EPT-CBR] [11]
  promoter TSS_2485 2312187 reverse nd [RS-EPT-CBR] [11]
  promoter TSS_2486 2312511 forward nd [RS-EPT-CBR] [11]
  promoter TSS_2487 2312654 forward nd [RS-EPT-CBR] [11]
  promoter TSS_2488 2312657 reverse nd [RS-EPT-CBR] [11]
  promoter TSS_2489 (cluster) 2316062 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [11]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Andersen J., Forst SA., Zhao K., Inouye M., Delihas N., 1989, The function of micF RNA. micF RNA is a major factor in the thermal regulation of OmpF protein in Escherichia coli., J Biol Chem 264(30):17961-70

 [2] Chen S., Lesnik EA., Hall TA., Sampath R., Griffey RH., Ecker DJ., Blyn LB., 2002, A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome., Biosystems 65(2-3):157-77

 [3] Delihas N., 1997, Antisense micF RNA and 5'-UTR of the target ompF RNA: phylogenetic conservation of primary and secondary structures., Nucleic Acids Symp Ser (36):33-5

 [4] Komatsu T., Ohta M., Kido N., Arakawa Y., Ito H., Mizuno T., Kato N., 1990, Molecular characterization of an Enterobacter cloacae gene (romA) which pleiotropically inhibits the expression of Escherichia coli outer membrane proteins., J Bacteriol 172(7):4082-9

 [5] Kumar A., Beloglazova N., Bundalovic-Torma C., Phanse S., Deineko V., Gagarinova A., Musso G., Vlasblom J., Lemak S., Hooshyar M., Minic Z., Wagih O., Mosca R., Aloy P., Golshani A., Parkinson J., Emili A., Yakunin AF., Babu M., 2016, Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli., Cell Rep 14(3):648-61

 [6] Mihailovic MK., Vazquez-Anderson J., Li Y., Fry V., Vimalathas P., Herrera D., Lease RA., Powell WB., Contreras LM., 2018, High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites., Nat Commun 9(1):4084

 [7] Tkachenko AG., Pozhidaeva ON., Shumkov MS., 2006, Role of polyamines in formation of multiple antibiotic resistance of Escherichia coli under stress conditions., Biochemistry (Mosc) 71(9):1042-9

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

 [9] Vogt SL., Evans AD., Guest RL., Raivio TL., 2014, The Cpx envelope stress response regulates and is regulated by small noncoding RNAs., J Bacteriol 196(24):4229-38

 [10] Zhang C., Chen S., Bai X., Dedkova LM., Hecht SM., 2020, Alteration of Transcriptional Regulator Rob In Vivo: Enhancement of Promoter DNA Binding and Antibiotic Resistance in the Presence of Nucleobase Amino Acids., Biochemistry 59(12):1217-1220

 [11] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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