RegulonDB RegulonDB 11.0: Gene Form
   

rmf gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pqiC fabA rmf pqiB CRP ppGpp terminator anti-terminator rmfp rmfp rmfp4 rmfp4 rmfp5 rmfp5

Gene      
Name: rmf    Texpresso search in the literature
Synonym(s): ECK0944, EG50004, b0953, res, rimF
Genome position(nucleotides): 1015715 --> 1015882
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.17
External database links:  
ASAP:
ABE-0003227
CGSC:
31760
ECHOBASE:
EB4298
ECOLIHUB:
rmf
OU-MICROARRAY:
b0953
STRING:
511145.b0953
COLOMBOS: rmf


Product      
Name: ribosome modulation factor
Synonym(s): Res, RimF, Rmf
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 6.507
Isoelectric point: 11.418
Motif(s):
 
Type Positions Sequence Comment
1 -> 52 MKRQKRDRLERAHQRGYQAGIAGRSKEMCPYQTLNQRSQWLGGWREAMADRV
3 -> 3 R UniProt: In Ref. 6; AA sequence..
25 -> 25 S UniProt: In Ref. 6; AA sequence..
33 -> 33 T UniProt: In Ref. 1; CAA49706..

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0043022 - ribosome binding
GO:0003723 - RNA binding
GO:0019843 - rRNA binding
GO:0043024 - ribosomal small subunit binding
biological_process GO:0006417 - regulation of translation
GO:0033554 - cellular response to stress
GO:0022611 - dormancy process
GO:0032055 - negative regulation of translation in response to stress
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[IEP] Inferred from expression pattern
[IMP] Inferred from mutant phenotype
Reference(s): [1] Aiso T., et al., 2005
[2] Apirakaramwong A., et al., 1999
[3] Bubunenko M., et al., 2007
[4] Chou CH., et al., 1996
[5] Ding Q., et al., 1996
[6] Ding Q., et al., 1997
[7] GeZi G., et al., 2021
[8] Imaizumi A., et al., 2005
[9] Raj VS., et al., 2001
[10] Terui Y., et al., 2010
[11] Tkachenko AG., et al., 2017
[12] Wada A., et al., 1995
[13] Yamagishi M., et al., 1993
External database links:  
ALPHAFOLD:
P0AFW2
DIP:
DIP-48260N
ECOCYC:
EG50004-MONOMER
ECOLIWIKI:
b0953
INTERPRO:
IPR007040
INTERPRO:
IPR023200
PDB:
4V8G
PDB:
6H4N
PDB:
6H58
PFAM:
PF04957
PRIDE:
P0AFW2
PRODB:
PRO_000023782
REFSEQ:
NP_415473
SMR:
P0AFW2
UNIPROT:
P0AFW2


Operon      
Name: rmf         
Operon arrangement:
Transcription unit        Promoter
rmf


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, SlyA, McbR, RcdA, SdiA
Repressed by: ArcA


RNA cis-regulatory element    
Attenuation: Transcriptional


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 rmfp5 1015503 forward nd [ICWHO] [14]
  promoter rmfp4 1015532 forward nd [ICWHO] [14]


Evidence    

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Aiso T., Yoshida H., Wada A., Ohki R., 2005, Modulation of mRNA stability participates in stationary-phase-specific expression of ribosome modulation factor., J Bacteriol 187(6):1951-8

 [2] Apirakaramwong A., Kashiwagi K., Raj VS., Sakata K., Kakinuma Y., Ishihama A., Igarashi K., 1999, Involvement of ppGpp, ribosome modulation factor, and stationary phase-specific sigma factor sigma(S) in the decrease in cell viability caused by spermidine., Biochem Biophys Res Commun 264(3):643-7

 [3] Bubunenko M., Baker T., Court DL., 2007, Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli., J Bacteriol 189(7):2844-53

 [4] Chou CH., Bennett GN., San KY., 1996, Genetic manipulation of stationary-phase genes to enhance recombinant protein production in Escherichia coli., Biotechnol Bioeng 50(6):636-42

 [5] Ding Q., Akira I., 1996, [Studies on modulation and control sigma 38 and RMF for the expression of some genes]., Wei Sheng Wu Xue Bao 36(5):344-50

 [6] Ding Q., Akira I., 1997, [Studies on selectivity of recognizing factor for rmf promoter]., Wei Sheng Wu Xue Bao 37(1):21-5

 [7] GeZi G., Liu R., Du D., Wu N., Bao N., Fan L., Morigen M., 2021, YfiF, an unknown protein, affects initiation timing of chromosome replication in Escherichia coli., J Basic Microbiol 61(10):883-899

 [8] Imaizumi A., Takikawa R., Koseki C., Usuda Y., Yasueda H., Kojima H., Matsui K., Sugimoto S., 2005, Improved production of L-lysine by disruption of stationary phase-specific rmf gene in Escherichia coli., J Biotechnol 117(1):111-8

 [9] Raj VS., Tomitori H., Yoshida M., Apirakaramwong A., Kashiwagi K., Takio K., Ishihama A., Igarashi K., 2001, Properties of a revertant of Escherichia coli viable in the presence of spermidine accumulation: increase in L-glycerol 3-phosphate., J Bacteriol 183(15):4493-8

 [10] Terui Y., Tabei Y., Akiyama M., Higashi K., Tomitori H., Yamamoto K., Ishihama A., Igarashi K., Kashiwagi K., 2010, Ribosome modulation factor, an important protein for cell viability encoded by the polyamine modulon., J Biol Chem 285(37):28698-707

 [11] Tkachenko AG., Kashevarova NM., Tyuleneva EA., Shumkov MS., 2017, Stationary-phase genes upregulated by polyamines are responsible for the formation of Escherichia coli persister cells tolerant to netilmicin., FEMS Microbiol Lett 364(9)

 [12] Wada A., Igarashi K., Yoshimura S., Aimoto S., Ishihama A., 1995, Ribosome modulation factor: stationary growth phase-specific inhibitor of ribosome functions from Escherichia coli., Biochem Biophys Res Commun 214(2):410-7

 [13] Yamagishi M., Matsushima H., Wada A., Sakagami M., Fujita N., Ishihama A., 1993, Regulation of the Escherichia coli rmf gene encoding the ribosome modulation factor: growth phase- and growth rate-dependent control., EMBO J 12(2):625-30

 [14] 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


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