RMF_ECOLI
ID RMF_ECOLI Reviewed; 55 AA.
AC P0AFW2; P22986; P77441;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Ribosome modulation factor {ECO:0000255|HAMAP-Rule:MF_00919, ECO:0000303|PubMed:2181444};
DE Short=RMF {ECO:0000255|HAMAP-Rule:MF_00919};
DE AltName: Full=Hibernation factor RMF {ECO:0000303|PubMed:22605777};
DE AltName: Full=Protein E;
GN Name=rmf {ECO:0000255|HAMAP-Rule:MF_00919, ECO:0000303|PubMed:2181444};
GN OrderedLocusNames=b0953, JW0936;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INDUCTION, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8440252; DOI=10.1002/j.1460-2075.1993.tb05695.x;
RA Yamagishi M., Matsushima H., Wada A., Sakagami M., Fujita N., Ishihama A.;
RT "Regulation of the Escherichia coli rmf gene encoding the ribosome
RT modulation factor: growth phase- and growth rate-dependent control.";
RL EMBO J. 12:625-630(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=2832401; DOI=10.1016/s0021-9258(18)68830-1;
RA Cronan J.E. Jr., Li W.-B., Coleman R., Narasimhan M., de Mendoza D.,
RA Schwab J.M.;
RT "Derived amino acid sequence and identification of active site residues of
RT Escherichia coli beta-hydroxydecanoyl thioester dehydrase.";
RL J. Biol. Chem. 263:4641-4646(1988).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP PROTEIN SEQUENCE OF 1-30, AND INTERACTION WITH 100S RIBOSOMES.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=2181444; DOI=10.1073/pnas.87.7.2657;
RA Wada A., Yamazaki Y., Fujita N., Ishihama A.;
RT "Structure and probable genetic location of a 'ribosome modulation factor'
RT associated with 100S ribosomes in stationary-phase Escherichia coli
RT cells.";
RL Proc. Natl. Acad. Sci. U.S.A. 87:2657-2661(1990).
RN [7]
RP FUNCTION.
RC STRAIN=K12 / W3350 / ATCC 27020;
RX PubMed=7677746; DOI=10.1006/bbrc.1995.2302;
RA Wada A., Igarashi K., Yoshimura S., Aimoto S., Ishihama A.;
RT "Ribosome modulation factor: stationary growth phase-specific inhibitor of
RT ribosome functions from Escherichia coli.";
RL Biochem. Biophys. Res. Commun. 214:410-417(1995).
RN [8]
RP INDUCTION.
RC STRAIN=K12;
RX PubMed=11532026; DOI=10.1046/j.1365-2443.2001.00457.x;
RA Izutsu K., Wada A., Wada C.;
RT "Expression of ribosome modulation factor (RMF) in Escherichia coli
RT requires ppGpp.";
RL Genes Cells 6:665-676(2001).
RN [9]
RP FUNCTION, AND INTERACTION WITH RIBOSOME.
RC STRAIN=K12;
RX PubMed=12473202; DOI=10.1093/oxfordjournals.jbchem.a003313;
RA Yoshida H., Maki Y., Kato H., Fujisawa H., Izutsu K., Wada C., Wada A.;
RT "The ribosome modulation factor (RMF) binding site on the 100S ribosome of
RT Escherichia coli.";
RL J. Biochem. 132:983-989(2002).
RN [10]
RP FUNCTION IN PROTECTION DURING HEAT STRESS.
RX PubMed=15278243; DOI=10.1007/s00203-004-0698-9;
RA Niven G.W.;
RT "Ribosome modulation factor protects Escherichia coli during heat stress,
RT but this may not be dependent on ribosome dimerisation.";
RL Arch. Microbiol. 182:60-66(2004).
RN [11]
RP FUNCTION, AND INTERACTION WITH RIBOSOME.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=15066119; DOI=10.1111/j.1356-9597.2004.00723.x;
RA Yoshida H., Yamamoto H., Uchiumi T., Wada A.;
RT "RMF inactivates ribosomes by covering the peptidyl transferase centre and
RT entrance of peptide exit tunnel.";
RL Genes Cells 9:271-278(2004).
RN [12]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=17277072; DOI=10.1128/jb.01713-06;
RA Bubunenko M., Baker T., Court D.L.;
RT "Essentiality of ribosomal and transcription antitermination proteins
RT analyzed by systematic gene replacement in Escherichia coli.";
RL J. Bacteriol. 189:2844-2853(2007).
RN [13]
RP FUNCTION.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=18174192; DOI=10.1093/jb/mvm243;
RA Ueta M., Ohniwa R.L., Yoshida H., Maki Y., Wada C., Wada A.;
RT "Role of HPF (hibernation promoting factor) in translational activity in
RT Escherichia coli.";
RL J. Biochem. 143:425-433(2008).
RN [14]
RP FUNCTION.
RX PubMed=19170772; DOI=10.1111/j.1365-2443.2008.01272.x;
RA Yoshida H., Ueta M., Maki Y., Sakai A., Wada A.;
RT "Activities of Escherichia coli ribosomes in IF3 and RMF change to prepare
RT 100S ribosome formation on entering the stationary growth phase.";
RL Genes Cells 14:271-280(2009).
RN [15]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / BW25113;
RX PubMed=26324267; DOI=10.1128/aac.01532-15;
RA McKay S.L., Portnoy D.A.;
RT "Ribosome hibernation facilitates tolerance of stationary-phase bacteria to
RT aminoglycosides.";
RL Antimicrob. Agents Chemother. 59:6992-6999(2015).
RN [16]
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) BOUND TO THE T.THERMOPHILUS 70S
RP RIBOSOME, FUNCTION, SUBUNIT, AND RRNA-BINDING.
RX PubMed=22605777; DOI=10.1126/science.1218538;
RA Polikanov Y.S., Blaha G.M., Steitz T.A.;
RT "How hibernation factors RMF, HPF, and YfiA turn off protein synthesis.";
RL Science 336:915-918(2012).
CC -!- FUNCTION: During stationary phase, converts 70S ribosomes to an
CC immature dimeric form (90S ribosomes) which are converted to inactive
CC 100S ribosomes (a process called ribosomal hibernation) by the
CC hibernation promoting factor HPF (PubMed:7677746, PubMed:18174192).
CC Inactivates ribosomes by covering the peptidyl transferase (PTase)
CC center of the 23S rRNA and the entrance of peptide exit tunnel
CC (PubMed:12473202, PubMed:15066119). However crystallization with
CC T.thermophilus 70S ribosomes shows it binds near the 3'-end of the 16S
CC rRNA near the anti-Shine-Dalgarno sequence, where it would sterically
CC hinder translation inititation (PubMed:22605777). In this crystal
CC binding of RMF induces movement of the 30S head domain away from the
CC rest of the ribosome, presumably so they would more easily form dimers
CC (PubMed:22605777). Also involved in protection against heat stress, but
CC this role is not dependent on the maintenance of ribosome dimers
CC (PubMed:15278243). {ECO:0000255|HAMAP-Rule:MF_00919,
CC ECO:0000269|PubMed:12473202, ECO:0000269|PubMed:15066119,
CC ECO:0000269|PubMed:15278243, ECO:0000269|PubMed:18174192,
CC ECO:0000269|PubMed:19170772, ECO:0000269|PubMed:7677746,
CC ECO:0000269|PubMed:8440252, ECO:0000269|PubMed:9278503}.
CC -!- SUBUNIT: Associates exclusively with 100S ribosomes (PubMed:2181444,
CC PubMed:12473202, PubMed:15066119). Contacts 16S rRNA, might contact
CC ribosomal protein S18 (PubMed:22605777). {ECO:0000269|PubMed:12473202,
CC ECO:0000269|PubMed:15066119, ECO:0000269|PubMed:2181444,
CC ECO:0000269|PubMed:22605777}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- INDUCTION: Induced during stationary growth phase (PubMed:8440252).
CC Requires ppGpp for translation (PubMed:11532026). {ECO:0000255|HAMAP-
CC Rule:MF_00919, ECO:0000269|PubMed:11532026,
CC ECO:0000269|PubMed:8440252}.
CC -!- DISRUPTION PHENOTYPE: Non-essential gene, 100S ribosome dimers are not
CC formed, decreased cell viability during stationary phase
CC (PubMed:8440252). A quadruple raiA-hpf-rmf-sra knockout strain is
CC significantly outcompeted by wild-type after 4 days growth
CC (PubMed:17277072). Very high sensitivity to aminoglycoside antiobiotic
CC gentamicin in stationary phase cultures (PubMed:26324267).
CC {ECO:0000269|PubMed:17277072, ECO:0000269|PubMed:26324267,
CC ECO:0000269|PubMed:8440252}.
CC -!- MISCELLANEOUS: When cells are transferred to rich nutritious culture
CC medium, RMF is quickly released from 100S ribosomes, which dissociate
CC into 70S ribosomes (PubMed:12473202). It indicates that this
CC interconversion is a major system regulating translation activity
CC during the transition of growth phases. {ECO:0000305|PubMed:12473202}.
CC -!- SIMILARITY: Belongs to the ribosome modulation factor family.
CC {ECO:0000255|HAMAP-Rule:MF_00919}.
CC -!- SEQUENCE CAUTION:
CC Sequence=J03186; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; X70111; CAA49706.1; -; Genomic_DNA.
DR EMBL; J03186; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; U00096; AAC74039.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35711.1; -; Genomic_DNA.
DR PIR; H64835; H64835.
DR RefSeq; NP_415473.1; NC_000913.3.
DR RefSeq; WP_000828648.1; NZ_STEB01000006.1.
DR PDB; 4V8G; X-ray; 3.00 A; AV/CV=1-55.
DR PDB; 6H4N; EM; 3.00 A; v=1-55.
DR PDB; 6H58; EM; 7.90 A; v/vv=1-55.
DR PDBsum; 4V8G; -.
DR PDBsum; 6H4N; -.
DR PDBsum; 6H58; -.
DR AlphaFoldDB; P0AFW2; -.
DR SMR; P0AFW2; -.
DR BioGRID; 4260019; 278.
DR BioGRID; 849941; 2.
DR DIP; DIP-48260N; -.
DR IntAct; P0AFW2; 4.
DR STRING; 511145.b0953; -.
DR jPOST; P0AFW2; -.
DR PaxDb; P0AFW2; -.
DR PRIDE; P0AFW2; -.
DR EnsemblBacteria; AAC74039; AAC74039; b0953.
DR EnsemblBacteria; BAA35711; BAA35711; BAA35711.
DR GeneID; 67414159; -.
DR GeneID; 945567; -.
DR KEGG; ecj:JW0936; -.
DR KEGG; eco:b0953; -.
DR PATRIC; fig|1411691.4.peg.1321; -.
DR EchoBASE; EB4298; -.
DR eggNOG; COG3130; Bacteria.
DR HOGENOM; CLU_203350_0_0_6; -.
DR InParanoid; P0AFW2; -.
DR OMA; EACPYQQ; -.
DR PhylomeDB; P0AFW2; -.
DR BioCyc; EcoCyc:EG50004-MON; -.
DR PRO; PR:P0AFW2; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoCyc.
DR GO; GO:0043024; F:ribosomal small subunit binding; IDA:EcoCyc.
DR GO; GO:0043022; F:ribosome binding; IDA:EcoCyc.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0032055; P:negative regulation of translation in response to stress; IDA:EcoCyc.
DR Gene3D; 1.10.10.620; -; 1.
DR HAMAP; MF_00919; RMF; 1.
DR InterPro; IPR007040; Ribosome_modulation_factor.
DR InterPro; IPR023200; RMF_sf.
DR Pfam; PF04957; RMF; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Reference proteome;
KW RNA-binding; rRNA-binding; Stress response; Translation regulation.
FT CHAIN 1..55
FT /note="Ribosome modulation factor"
FT /id="PRO_0000097363"
FT CONFLICT 3
FT /note="R -> I (in Ref. 6; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 25
FT /note="S -> V (in Ref. 6; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 33
FT /note="T -> S (in Ref. 1; CAA49706)"
FT /evidence="ECO:0000305"
FT HELIX 6..20
FT /evidence="ECO:0007829|PDB:4V8G"
FT STRAND 21..24
FT /evidence="ECO:0007829|PDB:4V8G"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:4V8G"
FT HELIX 35..49
FT /evidence="ECO:0007829|PDB:4V8G"
FT TURN 50..52
FT /evidence="ECO:0007829|PDB:4V8G"
SQ SEQUENCE 55 AA; 6507 MW; D264AF285BBF24AB CRC64;
MKRQKRDRLE RAHQRGYQAG IAGRSKEMCP YQTLNQRSQW LGGWREAMAD RVVMA
