Escherichia coli K-12 substr. MG1655 Polypeptide: ribosome modulation factor

Gene: rmf Accession Numbers: EG50004 (EcoCyc), b0953, ECK0944

Synonyms: res, rimF

Regulation Summary Diagram: ?

Regulation summary diagram for rmf

RMF is a ribosome modulation factor that reversibly converts active 70S ribosomes to a dimeric form, which appears during the transition from exponential growth to stationary phase and is associated with a decrease in overall translation activity [Wada90, Wada95]. Crystal structures of RMF associated with a Thermus thermophilus 70S ribosome showed that RMF binds to a site that overlaps with the binding site for the Shine-Dalgarno region of mRNA, thereby preventing mRNA interaction with the 16S subunit. Binding of RMF induces a conformational change that facilitates ribosome dimer formation [Polikanov12].

Purified RMF can cause dimerization of 70S ribosomes in vitro, inhibiting protein synthesis and binding of aminoacyl-tRNA to ribosomes. RMF specifically associates with 100S ribosomes in a 1:1 ratio and does not associate with 70S, 50S, and 30S ribosomal particles [Wada95]. RMF alone promotes dimerization to 90S ribosome particles; binding of HPF then promotes formation of 100S ribosome dimers [Ueta08]. RMF was reported to bind near the ribosomal proteins S13, L13, and L2, close to the peptidyl-tRNA binding site [Yoshida02], and to protect certain bases in the 23S rRNA, including A2451, which is thought to be involved in the peptidyl transferase activity [Yoshida04]. However, these results are contradicted by the results from crystallography [Polikanov12]. In late stationary phase, the ribosome dimers dissociate, which is followed by disassembly of the 70S ribosomes and loss of viability [Wada00].

Both RMF and ppGpp contribute to increased levels of noise in gene expression during stationary phase [Guido07].

An rmf mutant shows reduced viability during stationary phase and does not contain ribosome dimers [Yamagishi93, Wada00]. An rmf mutant is also heat sensitive in stationary phase [Niven04]. An rmf ompC double mutant and an rmf ompC rpoS triple mutant show even further reduced cell viability; this synthetic phenotype may be due to decreased levels of Mg2+ [Apirakaramwong98, Samuel02]. Genes whose expression is increased in an rmf mutant compared to wild type have been identified in a macroarray experiment [Imaizumi06].

Expression of rmf is induced at the transition from exponential growth to stationary phase or during slow growth; rmf expression appears to be inversely proportional to the growth rate [Yamagishi93]. Synthesis of Rmf is inhibited by high concentrations of spermidine inside the cell [Fukuchi95]. rmf expression is positively regulated by the stringent starvation factor ppGpp [Izutsu01a] and by cAMP-CRP [Shimada13]. The rmf mRNA is extremely stable during stationary phase, with a half life of approximately 24 minutes in early and 120 minutes in late stationary phase; transfer of the cells into fresh medium leads to an immediate drop in half life to approximately 5 minutes. rmf mRNA degradation requires RNA polymerase activity, RNase E, and PcnB. Transfer of stationary phase cells also causes Rmf protein levels to drop rapidly, and inactive ribosome dimers dissociate into active 70S ribosomes [Aiso05]. Translation of rmf is stimulated by polyamines via a structural change in the ribosome binding site [Terui10]. rmf expression is increased by acid stress [elSharoud05], and rmf influences survival of acid stress during stationary phase [ElSharoud07]. Depletion of the signal recognition particle receptor, FtsY, leads to upregulation of RMF levels, thus inhibiting translation [Burk09]. rmf was one of only three genes whose expression changed under all stress conditions tested by [Moen09].

Reviews: [Wada98a, Ishihama99, ElSharoud04]

Citations: [Apirakaramwong99, Bubunenko07, Yoshida09]

Locations: cytosol

Map Position: [1,014,938 -> 1,015,105] (21.88 centisomes, 79°)
Length: 168 bp / 55 aa

Molecular Weight of Polypeptide: 6.507 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003227 , CGSC:31760 , DIP:DIP-48260N , EchoBASE:EB4298 , EcoGene:EG50004 , EcoliWiki:b0953 , OU-Microarray:b0953 , PortEco:rmf , PR:PRO_000023782 , Pride:P0AFW2 , Protein Model Portal:P0AFW2 , RefSeq:NP_415473 , RegulonDB:EG50004 , SMR:P0AFW2 , String:511145.b0953 , UniProt:P0AFW2

Relationship Links: InterPro:IN-FAMILY:IPR007040 , InterPro:IN-FAMILY:IPR023200 , PDB:Structure:3V22 , PDB:Structure:3V24 , Pfam:IN-FAMILY:PF04957 , ProDom:IN-FAMILY:PD051650

Genetic Regulation Schematic: ?

Genetic regulation schematic for rmf

GO Terms:

Biological Process: GO:0032055 - negative regulation of translation in response to stress Inferred from experiment [Wada95]
GO:0033554 - cellular response to stress Inferred from experiment [Moen09]
GO:0006417 - regulation of translation Inferred by computational analysis [UniProtGOA11a, GOA06]
Molecular Function: GO:0043022 - ribosome binding Inferred from experiment [Wada90]
GO:0043024 - ribosomal small subunit binding Inferred from experiment [Polikanov12]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, Wada90, Azam00]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell structure ribosomes
information transfer protein related translation

Essentiality data for rmf knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Last-Curated ? 18-Mar-2013 by Keseler I , SRI International

Sequence Features

Protein sequence of ribosome modulation factor with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 3
[Wada90, UniProt10a]
UniProt: (in Ref. 6; AA sequence);
Sequence-Conflict 25
[Wada90, UniProt10a]
UniProt: (in Ref. 6; AA sequence);
Sequence-Conflict 33
[Yamagishi93, Cronan88, UniProt10a]
UniProt: (in Ref. 1 and 2);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


3/2/1998 (pkarp) Merged genes G250/b0953 and EG50004/rmf
10/20/97 Gene b0953 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG50004; confirmed by SwissProt match.


Aiso05: 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. PMID: 15743942

Apirakaramwong98: Apirakaramwong A, Fukuchi J, Kashiwagi K, Kakinuma Y, Ito E, Ishihama A, Igarashi K (1998). "Enhancement of cell death due to decrease in Mg2+ uptake by OmpC (cation-selective porin) deficiency in ribosome modulation factor-deficient mutant." Biochem Biophys Res Commun 251(2);482-7. PMID: 9792800

Apirakaramwong99: 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. PMID: 10543985

Azam00: Azam TA, Hiraga S, Ishihama A (2000). "Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid." Genes Cells 5(8);613-26. PMID: 10947847

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bubunenko07: 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. PMID: 17277072

Burk09: Burk J, Weiche B, Wenk M, Boy D, Nestel S, Heimrich B, Koch HG (2009). "Depletion of the signal recognition particle receptor inactivates ribosomes in Escherichia coli." J Bacteriol 191(22);7017-26. PMID: 19749044

Cronan88: Cronan JE, Li WB, Coleman R, Narasimhan M, de Mendoza D, Schwab JM (1988). "Derived amino acid sequence and identification of active site residues of Escherichia coli beta-hydroxydecanoyl thioester dehydrase." J Biol Chem 1988;263(10);4641-6. PMID: 2832401

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

ElSharoud04: El-Sharoud WM (2004). "Ribosome inactivation for preservation: concepts and reservations." Sci Prog 87(Pt 3);137-52. PMID: 15884656

elSharoud05: el-Sharoud WM, Niven GW (2005). "The activity of ribosome modulation factor during growth of Escherichia coli under acidic conditions." Arch Microbiol 184(1);18-24. PMID: 16088400

ElSharoud07: El-Sharoud WM, Niven GW (2007). "The influence of ribosome modulation factor on the survival of stationary-phase Escherichia coli during acid stress." Microbiology 153(Pt 1);247-53. PMID: 17185553

Fukuchi95: Fukuchi J, Kashiwagi K, Yamagishi M, Ishihama A, Igarashi K (1995). "Decrease in cell viability due to the accumulation of spermidine in spermidine acetyltransferase-deficient mutant of Escherichia coli." J Biol Chem 1995;270(32);18831-5. PMID: 7642535

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Guido07: Guido NJ, Lee P, Wang X, Elston TC, Collins JJ (2007). "A pathway and genetic factors contributing to elevated gene expression noise in stationary phase." Biophys J 93(11);L55-7. PMID: 17890398

Imaizumi06: Imaizumi A, Koseki C, Matsui K, Kojima H (2006). "Improved production of enzymes, which are expressed under the Pho regulon promoter, in the rmf gene (encoding ribosome modulation factor) disruptant of Escherichia coli." Biosci Biotechnol Biochem 70(4);949-57. PMID: 16636463

Ishihama99: Ishihama A (1999). "Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival." Genes Cells 4(3);135-43. PMID: 10320479

Izutsu01a: Izutsu K, Wada A, Wada C (2001). "Expression of ribosome modulation factor (RMF) in Escherichia coli requires ppGpp." Genes Cells 6(8);665-76. PMID: 11532026

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Moen09: Moen B, Janbu AO, Langsrud S, Langsrud O, Hobman JL, Constantinidou C, Kohler A, Rudi K (2009). "Global responses of Escherichia coli to adverse conditions determined by microarrays and FT-IR spectroscopy." Can J Microbiol 55(6);714-28. PMID: 19767843

Niven04: Niven GW (2004). "Ribosome modulation factor protects Escherichia coli during heat stress, but this may not be dependent on ribosome dimerisation." Arch Microbiol 182(1);60-6. PMID: 15278243

Polikanov12: Polikanov YS, Blaha GM, Steitz TA (2012). "How hibernation factors RMF, HPF, and YfiA turn off protein synthesis." Science 336(6083);915-8. PMID: 22605777

Samuel02: Samuel Raj V, Full C, Yoshida M, Sakata K, Kashiwagi K, Ishihama A, Igarashi K (2002). "Decrease in cell viability in an RMF, sigma(38), and OmpC triple mutant of Escherichia coli." Biochem Biophys Res Commun 299(2);252-7. PMID: 12437978

Shimada13: Shimada T, Yoshida H, Ishihama A (2013). "Involvement of cyclic AMP receptor protein in regulation of the rmf gene encoding the ribosome modulation factor in Escherichia coli." J Bacteriol 195(10);2212-9. PMID: 23475967

Terui10: 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. PMID: 20628056

Ueta08: Ueta M, Ohniwa RL, Yoshida H, Maki Y, Wada C, Wada A (2008). "Role of HPF (hibernation promoting factor) in translational activity in Escherichia coli." J Biochem 143(3);425-33. PMID: 18174192

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wada00: Wada A, Mikkola R, Kurland CG, Ishihama A (2000). "Growth phase-coupled changes of the ribosome profile in natural isolates and laboratory strains of Escherichia coli." J Bacteriol 182(10);2893-9. PMID: 10781560

Wada90: Wada A, Yamazaki Y, Fujita N, Ishihama A (1990). "Structure and probable genetic location of a "ribosome modulation factor" associated with 100S ribosomes in stationary-phase Escherichia coli cells." Proc Natl Acad Sci U S A 87(7);2657-61. PMID: 2181444

Wada95: 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. PMID: 7677746

Wada98a: Wada A (1998). "Growth phase coupled modulation of Escherichia coli ribosomes." Genes Cells 3(4);203-8. PMID: 9663655

Yamagishi93: 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. PMID: 8440252

Yoshida02: Yoshida H, Maki Y, Kato H, Fujisawa H, Izutsu K, Wada C, Wada A (2002). "The ribosome modulation factor (RMF) binding site on the 100S ribosome of Escherichia coli." J Biochem (Tokyo) 132(6);983-9. PMID: 12473202

Yoshida04: Yoshida H, Yamamoto H, Uchiumi T, Wada A (2004). "RMF inactivates ribosomes by covering the peptidyl transferase centre and entrance of peptide exit tunnel." Genes Cells 9(4);271-8. PMID: 15066119

Yoshida09: Yoshida H, Ueta M, Maki Y, Sakai A, Wada A (2009). "Activities of Escherichia coli ribosomes in IF3 and RMF change to prepare 100S ribosome formation on entering the stationary growth phase." Genes Cells 14(2);271-80. PMID: 19170772

Other References Related to Gene Regulation

Maki00: Maki Y, Yoshida H, Wada A (2000). "Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli." Genes Cells 2000;5(12);965-74. PMID: 11168583

Raivio13: Raivio TL, Leblanc SK, Price NL (2013). "The Escherichia coli Cpx envelope stress response regulates genes of diverse function that impact antibiotic resistance and membrane integrity." J Bacteriol 195(12);2755-67. PMID: 23564175

Teramoto10: Teramoto J, Yamanishi Y, Magdy el-SH, Hasegawa A, Kori A, Nakajima M, Arai F, Fukuda T, Ishihama A (2010). "Single live-bacterial cell assay of promoter activity and regulation." Genes Cells 15(11);1111-22. PMID: 20964794

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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