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Escherichia coli K-12 substr. MG1655 Protein: HipB antitoxin and DNA-binding transcriptional repressor
Inferred from experiment



Gene: hipB Accession Numbers: EG10442 (EcoCyc), b1508, ECK1501

Regulation Summary Diagram

Regulation summary diagram for hipB

Component of: HipAB toxin/antitoxin complex and DNA-binding transcriptional repressor (extended summary available)

Subunit composition of HipB antitoxin and DNA-binding transcriptional repressor = [HipB]2
         HipB antitoxin and DNA-binding transcriptional repressor = HipB

Summary:
HipB is a transcriptional repressor that functions as the antagonist of HipA, which was the first protein found to mediate the phenomenon of persistence in E. coli. A small fraction of cells within a population are dormant persister cells; these cells are phenotypic variants that are not killed by antibiotics, leading to multidrug tolerance (MDT). Persistence may be ultimately due to global remodeling of the persister cell's ribosomes [Cho15]. The HipAB system can be categorized as a type II toxin/antitoxin module.

In the absence of its binding partner HipB, HipA is toxic to the cell [Black91, Black94, Rotem10]. Above a certain threshold, the level of HipA in the cell determines the typical duration of growth arrest. The threshold level is determined by the level of HipB [Rotem10]. The HipAB system appears to be regulated at the level of HipB stability. Degradation of HipB is mainly dependent on the Lon protease, and is dependent on an unstructured 16 amino acid domain at the C terminus of the protein [Hansen12].

A variety of crystal structures of HipB in complexes with DNA and HipA have been solved [Schumacher09, Evdokimov09, Schumacher12, Schumacher15]. Binding to HipB may lock HipA into a catalytically inactive conformation [Schumacher09]. The crystal structure of an extended promoter region that contained two operator sites revealed that the interaction with HipB dimers bound to both sites leads to dimerizarion of HipA, which blocks the active sites of both HipA molecules [Schumacher15].

The HipA-mediated phenotypic switch has been investigated at the single cell level [Balaban04], and mathematical models have been developed [Lou08, Koh12], suggesting that phenotypic variation in persister levels within a population can be due to different levels of noise in the regulation of the gene circuit [Koh12]. The bistability of the HipBA system has been successfully simulated with a stochastic model that includes reciprocal coupling of free HipA to the cellular growth rate [Feng14]. Above a certain threshold, the level of HipA in the cell determines the typical duration of growth arrest. The threshold level is determined by the level of HipB [Rotem10].

Expression of the hipBA operon is autoregulated. HipB binds with high affinity to four instances of the palindromic sequence TATCCN8GGATA within the hipBA promoter region [Black94]. Bioinformatic analysis revealed that there are a total of 39 potential HipB-binding sequences in the promoter regions of 33 genes in the E. coli genome, including relA, eutH, and fadH, which were experimentally verified. In addition, HipA enhances repression of the relA promoter by HipB [Lin13a].

A hipBA deletion strain shows a decrease in stationary phase persister cells after treatment with antibiotics [Keren04] and a decrease in biofilm formation even in the absence of antibiotics [Zhao13]. Expression of wild-type hipA in excess of hipB results in the shutdown of macromolecular synthesis and a high frequency of persister formation [Korch06].

HipB: "high persistence" [Moyed83]

Reviews: [Maisonneuve14, Kahrstrom13, Brzozowska13, Yamaguchi11, Lewis08, Jayaraman08, Lewis07, Lewis05a]

Citations: [Hendricks00, Li13]

Locations: cytosol

Map Position: [1,590,200 <- 1,590,466] (34.27 centisomes, 123°)
Length: 267 bp / 88 aa

Molecular Weight of Polypeptide: 10.016 kD (from nucleotide sequence), 10.0 kD (experimental) [Black91]

Molecular Weight of Multimer: 26.0 kD (experimental) [Black94]

Unification Links: ASAP:ABE-0005024, EchoBASE:EB0437, EcoGene:EG10442, EcoliWiki:b1508, ModBase:P23873, OU-Microarray:b1508, PortEco:hipB, PR:PRO_000022890, Protein Model Portal:P23873, RefSeq:NP_416025, RegulonDB:EG10442, SMR:P23873, String:511145.b1508, UniProt:P23873

Relationship Links: InterPro:IN-FAMILY:IPR001387, InterPro:IN-FAMILY:IPR010982, PDB:RELATED-TO:3DNV, PDB:Structure:2WIU, PDB:Structure:3HZI, Pfam:IN-FAMILY:PF01381, Prosite:IN-FAMILY:PS50943, Smart:IN-FAMILY:SM00530

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for hipB


GO Terms:
Biological Process:
Inferred from experimentInferred by computational analysisGO:0006351 - transcription, DNA-templated [UniProtGOA11a, Black94]
Inferred from experimentGO:0045892 - negative regulation of transcription, DNA-templated [Black94]
Inferred by computational analysisGO:0006355 - regulation of transcription, DNA-templated [UniProtGOA11a]
Molecular Function:
Inferred from experimentGO:0000985 - bacterial-type RNA polymerase core promoter sequence-specific DNA binding [Black94]
Inferred from experimentGO:0005515 - protein binding [Black94]
Inferred from experimentGO:0042803 - protein homodimerization activity [Black94]
Inferred from experimentInferred by computational analysisGO:0043565 - sequence-specific DNA binding [GOA01a, Black94]
Inferred by computational analysisGO:0003677 - DNA binding [UniProtGOA11a, GOA01a]
Cellular Component:
Inferred by curatorGO:0005829 - cytosol []

MultiFun Terms: information transferRNA relatedTranscription related
regulationtype of regulationtranscriptional levelrepressor

DNA binding site length: 20 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: tTATCCgctatagcGGATAa

Regulated Transcription Units (4 total):

Notes:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Essentiality data for hipB knockouts:

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

Credits:
Created 05-Feb-2009 by Keseler I, SRI International
Last-Curated 16-Sep-2015 by Keseler I, SRI International


Subunit of: HipAB toxin/antitoxin complex and DNA-binding transcriptional repressor

Inferred from experiment

Synonyms: HipBA

Subunit composition of HipAB toxin/antitoxin complex and DNA-binding transcriptional repressor = [(HipB)2][HipA]
         HipB antitoxin and DNA-binding transcriptional repressor = (HipB)2
                 HipB antitoxin and DNA-binding transcriptional repressor = HipB
         serine/threonine kinase HipA = HipA (extended summary available)

Summary:
The transcriptional repressor HipB, for "High persistence," is negatively autoregulated and controls the transcription of a critical persistence factor [Kawano09, Lewis05a, Keren04, Black91, Korch03, Balaban04]. hipB foms an operon with hipA, and the products of this operon are classified as a toxin (HipA)-antitoxin (HipB) system. This HipAB system is involved in the high persistence, which is the capacity of the bacteria to survive prolonged exposure to antibiotics [Balaban04, Inouye06], and Kawano et al. also showed that this system is important for survival during the long-term stationary phase [Kawano09, Lewis05a, Keren04].

The crystal structure of the HipB-HipA-DNA complex has been solved at 2.68 Å resolution [Schumacher09]. The complex is tetrameric and is comprised of a HipB homodimer that interacts with DNA, sandwiched by a monomer of HipA on each side [Schumacher09]. In the HipB-HipA complex, each monomer of HipA interacts with two monomers of HipB [Schumacher09, Evdokimov09]. The crystal structure of an extended promoter region that contained two operator sites revealed that the interaction with HipB bound to both sites leads to dimerizarion of HipA, which blocks the active sites of both HipA molecules [Schumacher15].

HipB is an antitoxin that counteracts and neutralizes the HipA toxin, and HipA is toxic in the absence of its binding partner HipB [Schumacher09, Black94, Black91]. Although HipA does not bind the Hip regulatory region, it plays an indirect role via its binding to HipB.

HipB contains a helix-turn-helix motif near the N terminus and is a Cro-like DNA-binding protein. It binds to four operator sites with the conserved inverted repeat sequence motif TATCCN8GGATA, and its binding occurs cooperatively and almost simultaneously on the same face of the DNA helix. HipB forms dimers in solution [Black94, Schumacher09].

Reviews: [Yamaguchi11, Jayaraman08]

Citations: [Li13]

Relationship Links: PDB:Structure:3DNV, PDB:Structure:3DNW


GO Terms:
Biological Process:
Inferred from experimentGO:0045892 - negative regulation of transcription, DNA-templated [Black94]
Molecular Function:
Inferred from experimentGO:0043565 - sequence-specific DNA binding [Black94]

DNA binding site length: 20 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: tTATCCgctatAGCGGATAa

Regulated Transcription Units (2 total):

Notes:

Transcription-unit diagram

Transcription-unit diagram


Sequence Features

Protein sequence of HipB antitoxin and DNA-binding transcriptional repressor with features indicated

Feature Class Location Citations Comment
Conserved-Region 17 -> 71
Inferred from experiment[Schumacher09]
UniProt: HTH cro/C1-type.
Pfam PF01381 18 -> 69
Inferred by computational analysis[Finn14]
HTH_3 : Helix-turn-helix
DNA-Binding-Region 21 -> 47
Inferred from experiment[Schumacher09]
UniProt: H-T-H motif.
Mutagenesis-Variant 73 -> 88
Inferred from experiment[Hansen12]
UniProt: Increased half-life in vivo and in vitro, no change in DNA or HipA-binding.
Mutagenesis-Variant 88
Inferred from experiment[Hansen12]
UniProt: No change in DNA or HipA-binding.


Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram

Notes:

History:
1/26/1998 (pkarp) Merged genes G7994/hipB and EG10442/hipB


References

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

Balaban04: Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S (2004). "Bacterial persistence as a phenotypic switch." Science 305(5690);1622-5. PMID: 15308767

Black91: Black DS, Kelly AJ, Mardis MJ, Moyed HS (1991). "Structure and organization of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis." J Bacteriol 173(18);5732-9. PMID: 1715862

Black94: Black DS, Irwin B, Moyed HS (1994). "Autoregulation of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis." J Bacteriol 1994;176(13);4081-91. PMID: 8021189

Brzozowska13: Brzozowska I, Zielenkiewicz U (2013). "Regulation of toxin-antitoxin systems by proteolysis." Plasmid 70(1);33-41. PMID: 23396045

Cho15: Cho J, Rogers J, Kearns M, Leslie M, Hartson SD, Wilson KS (2015). "Escherichia coli persister cells suppress translation by selectively disassembling and degrading their ribosomes." Mol Microbiol 95(2);352-64. PMID: 25425348

Evdokimov09: Evdokimov A, Voznesensky I, Fennell K, Anderson M, Smith JF, Fisher DA (2009). "New kinase regulation mechanism found in HipBA: a bacterial persistence switch." Acta Crystallogr D Biol Crystallogr 65(Pt 8);875-9. PMID: 19622872

Feng14: Feng J, Kessler DA, Ben-Jacob E, Levine H (2014). "Growth feedback as a basis for persister bistability." Proc Natl Acad Sci U S A 111(1);544-9. PMID: 24344277

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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

Hansen12: Hansen S, Vulic M, Min J, Yen TJ, Schumacher MA, Brennan RG, Lewis K (2012). "Regulation of the Escherichia coli HipBA Toxin-Antitoxin System by Proteolysis." PLoS One 7(6);e39185. PMID: 22720069

Hendricks00: Hendricks EC, Szerlong H, Hill T, Kuempel P (2000). "Cell division, guillotining of dimer chromosomes and SOS induction in resolution mutants (dif, xerC and xerD) of Escherichia coli." Mol Microbiol 36(4);973-81. PMID: 10844683

Inouye06: Inouye M (2006). "The discovery of mRNA interferases: implication in bacterial physiology and application to biotechnology." J Cell Physiol 209(3);670-6. PMID: 17001682

Jayaraman08: Jayaraman R (2008). "Bacterial persistence: some new insights into an old phenomenon." J Biosci 33(5);795-805. PMID: 19179767

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

Kahrstrom13: Kahrstrom CT (2013). "Bacterial physiology: a persistent magic spot." Nat Rev Microbiol 11(11);739. PMID: 24056929

Kawano09: Kawano H, Hirokawa Y, Mori H (2009). "Long-term survival of Escherichia coli lacking the HipBA toxin-antitoxin system during prolonged cultivation." Biosci Biotechnol Biochem 73(1);117-23. PMID: 19129642

Keren04: Keren I, Shah D, Spoering A, Kaldalu N, Lewis K (2004). "Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli." J Bacteriol 186(24);8172-80. PMID: 15576765

Koh12: Koh RS, Dunlop MJ (2012). "Modeling suggests that gene circuit architecture controls phenotypic variability in a bacterial persistence network." BMC Syst Biol 6;47. PMID: 22607777

Korch03: Korch SB, Henderson TA, Hill TM (2003). "Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis." Mol Microbiol 50(4);1199-213. PMID: 14622409

Korch06: Korch SB, Hill TM (2006). "Ectopic overexpression of wild-type and mutant hipA genes in Escherichia coli: effects on macromolecular synthesis and persister formation." J Bacteriol 188(11);3826-36. PMID: 16707675

Lewis05a: Lewis K (2005). "Persister cells and the riddle of biofilm survival." Biochemistry (Mosc) 70(2);267-74. PMID: 15807669

Lewis07: Lewis K (2007). "Persister cells, dormancy and infectious disease." Nat Rev Microbiol 5(1);48-56. PMID: 17143318

Lewis08: Lewis K (2008). "Multidrug tolerance of biofilms and persister cells." Curr Top Microbiol Immunol 322;107-31. PMID: 18453274

Li13: Li C, Wang Y, Chen G (2013). "Interaction investigations of HipA binding to HipB dimer and HipB dimer + DNA complex: a molecular dynamics simulation study." J Mol Recognit 26(11);556-67. PMID: 24089363

Lin13a: Lin CY, Awano N, Masuda H, Park JH, Inouye M (2013). "Transcriptional Repressor HipB Regulates the Multiple Promoters in Escherichia coli." J Mol Microbiol Biotechnol 23(6);440-447. PMID: 24089053

Lou08: Lou C, Li Z, Ouyang Q (2008). "A molecular model for persister in E. coli." J Theor Biol 255(2);205-9. PMID: 18721814

Maisonneuve14: Maisonneuve E, Gerdes K (2014). "Molecular mechanisms underlying bacterial persisters." Cell 157(3);539-48. PMID: 24766804

Moyed83: Moyed HS, Bertrand KP (1983). "hipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis." J Bacteriol 155(2);768-75. PMID: 6348026

Rotem10: Rotem E, Loinger A, Ronin I, Levin-Reisman I, Gabay C, Shoresh N, Biham O, Balaban NQ (2010). "Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence." Proc Natl Acad Sci U S A 107(28);12541-6. PMID: 20616060

Schumacher09: Schumacher MA, Piro KM, Xu W, Hansen S, Lewis K, Brennan RG (2009). "Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB." Science 323(5912);396-401. PMID: 19150849

Schumacher12: Schumacher MA, Min J, Link TM, Guan Z, Xu W, Ahn YH, Soderblom EJ, Kurie JM, Evdokimov A, Moseley MA, Lewis K, Brennan RG (2012). "Role of unusual P loop ejection and autophosphorylation in HipA-mediated persistence and multidrug tolerance." Cell Rep 2(3);518-25. PMID: 22999936

Schumacher15: Schumacher MA, Balani P, Min J, Chinnam NB, Hansen S, Vulic M, Lewis K, Brennan RG (2015). "HipBA-promoter structures reveal the basis of heritable multidrug tolerance." Nature 524(7563);59-64. PMID: 26222023

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

Yamaguchi11: Yamaguchi Y, Park JH, Inouye M (2011). "Toxin-antitoxin systems in bacteria and archaea." Annu Rev Genet 45;61-79. PMID: 22060041

Zhao13: Zhao J, Wang Q, Li M, Heijstra BD, Wang S, Liang Q, Qi Q (2013). "Escherichia coli toxin gene hipA affects biofilm formation and DNA release." Microbiology 159(Pt 3);633-40. PMID: 23329678


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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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