RegulonDB

Gene
Name:	micF
Synonym(s):	ECK2208, EG30063, b4439, stc
Genome position(nucleotides):	2313084 --> 2313176
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:0009410 - response to xenobiotic stimulus GO:0040033 - RNA-mediated gene silencing by inhibition of translation GO:0034605 - cellular response to heat GO:0071474 - cellular hyperosmotic response

Note(s):

Note(s): ...[more].

Evidence:

[EXP] Inferred from experiment
[EXP-IDA] Inferred from direct assay

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	micFp1
micF	micFp2

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

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

Type	Name	Post Left	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	nd	[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.