RegulonDB

Gene
Name:	rmf
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:

[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IEP] Inferred from expression pattern
[EXP-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:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

PDB:

PDB:

PDB:

PFAM:

PRIDE:

PRODB:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

rmf

Operon arrangement:

Transcription unit	Promoter
rmf	rmfp

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	[COMP-AINF]	[14]
	promoter	rmfp4	1015532		forward	nd	[COMP-AINF]	[14]

Evidence
[COMP-AINF] 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