Escherichia coli K-12 substr. MG1655 Polypeptide: hibernation promoting factor

Gene: hpf Accession Numbers: EG11681 (EcoCyc), b3203, ECK3192

Synonyms: yhbH

Regulation Summary Diagram: ?

Regulation summary diagram for hpf

Hibernation promoting factor (HPF) binds to 100S ribosome dimers at stationary phase [Maki00]. RMF alone promotes dimerization of 70S ribosomes to 90S ribosome particles; binding of HPF then promotes formation of stable 100S ribosome dimers [Ueta08].

Crystal structures of HPF associated with a Thermus thermophilus 70S ribosome showed that both HPF and YfiA bind in the channel between the head and body of the 30S ribosomal subunit, apparently blocking the sites for tRNA and mRNA binding during protein synthesis. The binding site also overlaps with the binding sites for IF1 and IF3 as well as EF-G, which are all involved in dissociation of the ribosomal subunits [Polikanov12]. An NMR solution structure of HPF alone is also available [Sato09].

Binding of HPF to the ribosome inhibits translation in some in vitro assays [Ueta08].

Expression of hpf is induced by the autoinducer 2 (AI-2) quorum sensing pheromone [DeLisa01].

In a hpf yfiA double deletion mutant, only 90S ribosome particles are found in stationary phase [Ueta05].

Hpf: "hibernation promoting factor" [Ueta05]

Review: [ElSharoud04]

Citations: [Bubunenko07, Yoshida09]

Gene Citations: [Rhodius05, Jones94a]

Locations: cytosol

Map Position: [3,344,195 -> 3,344,482] (72.08 centisomes, 259°)
Length: 288 bp / 95 aa

Molecular Weight of Polypeptide: 10.75 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010516 , DIP:DIP-48273N , EchoBASE:EB1632 , EcoGene:EG11681 , EcoliWiki:b3203 , Mint:MINT-1249576 , ModBase:P0AFX0 , OU-Microarray:b3203 , PortEco:hpf , Pride:P0AFX0 , Protein Model Portal:P0AFX0 , RefSeq:NP_417670 , RegulonDB:EG11681 , SMR:P0AFX0 , String:511145.b3203 , UniProt:P0AFX0

Relationship Links: InterPro:IN-FAMILY:IPR003489 , PDB:Structure:2RQL , PDB:Structure:3V26 , PDB:Structure:3V28 , Pfam:IN-FAMILY:PF02482

GO Terms:

Biological Process: GO:0017148 - negative regulation of translation Inferred from experiment [Ueta08]
GO:0006417 - regulation of translation Inferred by computational analysis [UniProtGOA11]
GO:0044238 - primary metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0043022 - ribosome binding Inferred from experiment [Maki00]
GO:0043024 - ribosomal small subunit binding Inferred from experiment [Polikanov12]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: information transfer protein related translation

Essentiality data for hpf knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Last-Curated ? 01-Jun-2012 by Keseler I , SRI International

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3203 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11681; confirmed by SwissProt match.


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

DeLisa01: DeLisa MP, Wu CF, Wang L, Valdes JJ, Bentley WE (2001). "DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli." J Bacteriol 183(18);5239-47. PMID: 11514505

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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Jones94a: Jones DH, Franklin FC, Thomas CM (1994). "Molecular analysis of the operon which encodes the RNA polymerase sigma factor sigma 54 of Escherichia coli." Microbiology 1994;140 ( Pt 5);1035-43. PMID: 8025669

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

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

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

Rhodius05: Rhodius VA, Suh WC, Nonaka G, West J, Gross CA (2005). "Conserved and variable functions of the sigmaE stress response in related genomes." PLoS Biol 4(1);e2. PMID: 16336047

Sato09: Sato A, Watanabe T, Maki Y, Ueta M, Yoshida H, Ito Y, Wada A, Mishima M (2009). "Solution structure of the E. coli ribosome hibernation promoting factor HPF: Implications for the relationship between structure and function." Biochem Biophys Res Commun 389(4);580-5. PMID: 19747895

Ueta05: Ueta M, Yoshida H, Wada C, Baba T, Mori H, Wada A (2005). "Ribosome binding proteins YhbH and YfiA have opposite functions during 100S formation in the stationary phase of Escherichia coli." Genes Cells 10(12);1103-12. PMID: 16324148

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

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

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

Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324

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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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